Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4239576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 13460.65 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4239576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 4239.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4239576 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.10u 0.02s 00:00:00.12 Elapsed: 00:00:00.07 # Mc/sec: 9448.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4239576 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.19u 0.02s 00:00:00.21 Elapsed: 00:00:00.15 # Mc/sec: 11899.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4239576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 8903.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-19 58.6 0.0 4.8e-14 41.5 0.0 2.7 1 frame_2 Domain annotation for each sequence: >> frame_2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 41.5 0.0 7.9e-15 4.8e-14 1 168 [] 653992 654147 .. 653992 654147 .. 0.89 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4239576 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.85u 0.03s 00:00:00.88 Elapsed: 00:00:00.82 # Mc/sec: 868.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4239576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 3674.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4239576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.11u 0.02s 00:00:00.13 Elapsed: 00:00:00.07 # Mc/sec: 21319.01 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178611.0.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (981070 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 3060.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (981070 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 8633.42 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (981070 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 5150.62 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-15 44.5 0.0 9.3e-15 43.8 0.0 1.4 1 frame_2 Domain annotation for each sequence: >> frame_2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 43.8 0.0 1.6e-15 9.3e-15 1 168 [] 84489 84644 .. 84489 84644 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (981070 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.19u 0.02s 00:00:00.21 Elapsed: 00:00:00.21 # Mc/sec: 784.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (981070 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6229.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (981070 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05 # Mc/sec: 8260.61 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (981070 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 1962.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (981070 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 1275.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000011.9.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1178.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (108196 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3808.50 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (108196 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (108196 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4555.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (108196 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1374.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (108196 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 281.31 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (108196 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1817.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (108196 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1136.06 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000231.99.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (108196 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (23032 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 810.73 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (23032 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (23032 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (23032 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (23032 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 386.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (23032 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (23032 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000091.100.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (23032 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (95412 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (95412 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (95412 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 381.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (95412 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (95412 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (95412 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (95412 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000441.101.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (95412 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (9932 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (9932 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (9932 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (9932 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (9932 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (9932 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (9932 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 154.94 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000061.102.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (9932 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (31936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (31936 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (31936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1124.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (31936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (31936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 335.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (31936 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (31936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 405.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000411.103.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (31936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (28706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (28706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 301.41 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (28706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (28706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (28706 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (28706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (28706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000011.104.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (28706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (116676 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 303.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (116676 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (116676 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1960.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (116676 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (116676 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (116676 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (116676 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4107.00 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832591.105.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (116676 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (189368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2954.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (189368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (189368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6665.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (189368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7972.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (189368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (189368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 757.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (189368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832621.106.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (189368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (123448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (123448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5197.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (123448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (123448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (123448 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (123448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (123448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832631.107.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (123448 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1296.20 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (130474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2035.39 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (130474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1657.02 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (130474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (130474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (130474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (130474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (130474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000131.108.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (130474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 339.23 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (145054 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2436.91 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (145054 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (145054 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1523.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (145054 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 580.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (145054 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 5105.90 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (145054 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (145054 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000131.10.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (145054 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (407986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6854.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (407986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (407986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (407986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 17176.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (407986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (407986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4283.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (407986 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 3182.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000211.109.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (407986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 14361.11 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (87302 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1108.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (87302 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1466.67 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (87302 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (87302 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (87302 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3675.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (87302 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 916.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (87302 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000701.110.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (87302 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 349.21 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (33274 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (33274 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (33274 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (33274 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (33274 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 349.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (33274 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (33274 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1171.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000051.111.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (33274 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1400.84 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (90208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (90208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3797.76 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (90208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (90208 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1407.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (90208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (90208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (90208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000361.112.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (90208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (68996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2904.73 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (68996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 876.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (68996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (68996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (68996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 724.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (68996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (68996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 275.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000261.113.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (68996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (279786 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4700.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (279786 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 1776.64 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (279786 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (279786 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 4924.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (279786 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (279786 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (279786 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4364.66 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832611.114.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (279786 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11778.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (312528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6578.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (312528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (312528 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4875.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-15 46.1 0.0 3.3e-15 45.3 0.0 1.4 1 frame_1 Domain annotation for each sequence: >> frame_1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 45.3 0.0 5.6e-16 3.3e-15 1 168 [] 17031 17186 .. 17031 17186 .. 0.89 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (312528 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.08u 0.00s 00:00:00.08 Elapsed: 00:00:00.09 # Mc/sec: 583.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (312528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 5500.49 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (312528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3969.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (312528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1250.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (312528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3281.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000341.115.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (365374 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7691.12 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (365374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (365374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6138.28 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (365374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5699.83 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (365374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12861.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (365374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4640.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (365374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000041.116.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (365374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3836.43 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (96068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (96068 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1498.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (96068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3381.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (96068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (96068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (96068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (96068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000641.117.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (96068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (230082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (230082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2922.04 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (230082 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3589.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (230082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 920.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (230082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2415.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (230082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9686.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (230082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3865.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000101.118.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (230082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8098.89 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (567998 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5963.98 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (567998 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1476.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (567998 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7213.57 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (567998 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9542.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (567998 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 11956.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (567998 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 4430.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (567998 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 19993.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000021.11.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (567998 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2271.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-42 131.6 6.2 1.1e-41 131.2 6.2 1.2 1 frame_4 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 131.2 6.2 1.8e-42 1.1e-41 3 352 .] 219738 220098 .. 219736 220098 .. 0.87 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4020662 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 1.55u 0.03s 00:00:01.58 Elapsed: 00:00:01.51 # Mc/sec: 937.27 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4020662 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 10554.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4020662 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.22u 0.02s 00:00:00.24 Elapsed: 00:00:00.14 # Mc/sec: 12090.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4020662 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 2613.43 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4020662 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.19u 0.03s 00:00:00.22 Elapsed: 00:00:00.10 # Mc/sec: 6272.23 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-19 58.9 0.0 1.2e-14 43.5 0.0 2.8 1 frame_2 Domain annotation for each sequence: >> frame_2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 43.5 0.0 1.9e-15 1.2e-14 1 168 [] 250887 251042 .. 250887 251042 .. 0.91 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4020662 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.82u 0.02s 00:00:00.84 Elapsed: 00:00:00.79 # Mc/sec: 855.03 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4020662 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.06 # Mc/sec: 8510.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4020662 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 5360.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF13575.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF13575.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: DUF4135 [M=377] Accession: PF13575.8 Description: Domain of unknown function (DUF4135) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (377 nodes) Target sequences: 6 (42156 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1589.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/lanl.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.lanl.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: lanl [M=55] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (55 nodes) Target sequences: 6 (42156 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF04738.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF04738.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_N [M=650] Accession: PF04738.15 Description: Lantibiotic dehydratase, N terminus Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-146 475.2 0.0 9.4e-146 475.0 0.0 1.0 1 AOIprotein6 Domain annotation for each sequence: >> AOIprotein6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 475.0 0.0 1.6e-146 9.4e-146 2 647 .. 3772 4417 .. 3771 4420 .. 0.95 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (650 nodes) Target sequences: 6 (42156 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.07 # Mc/sec: 391.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000011.119.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-56 179.2 0.0 6.4e-56 178.8 0.0 1.1 1 AOIprotein5 Domain annotation for each sequence: >> AOIprotein5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.8 0.0 1.1e-56 6.4e-56 1 287 [. 4476 4744 .. 4476 4745 .. 0.92 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (42156 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 607.05 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-23 70.2 0.0 1.1e-22 69.6 0.0 1.3 1 frame_5 Domain annotation for each sequence: >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 69.6 0.0 1.9e-23 1.1e-22 1 168 [] 113513 113678 .. 113513 113678 .. 0.94 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1521934 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.32u 0.01s 00:00:00.33 Elapsed: 00:00:00.33 # Mc/sec: 774.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1521934 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 659.50 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1521934 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 16018.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1521934 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 7914.06 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1521934 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 3043.87 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1521934 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 13393.02 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1521934 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 7990.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1521934 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9664.28 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NHRV010000021.120.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1735706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 9112.46 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1735706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 2256.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1735706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 9719.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1735706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 11021.73 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1735706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6942.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1735706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 13538.51 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1735706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 36536.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145981.121.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1735706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.03 # Mc/sec: 20365.62 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4560520 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.20u 0.03s 00:00:00.23 Elapsed: 00:00:00.15 # Mc/sec: 4742.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-14 42.9 0.0 2.7e-14 42.3 0.0 1.3 1 frame_4 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 42.3 0.0 4.5e-15 2.7e-14 1 168 [] 2069 2224 .. 2069 2224 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4560520 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.91u 0.02s 00:00:00.93 Elapsed: 00:00:00.87 # Mc/sec: 880.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4560520 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 2964.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4560520 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.13u 0.02s 00:00:00.15 Elapsed: 00:00:00.07 # Mc/sec: 22932.90 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4560520 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.06 # Mc/sec: 7980.91 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4560520 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 4560.52 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4560520 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.27u 0.02s 00:00:00.29 Elapsed: 00:00:00.15 # Mc/sec: 12799.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4560520 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.09u 0.01s 00:00:00.10 Elapsed: 00:00:00.07 # Mc/sec: 8274.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (33336 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (33336 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1073.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_AP0145971.122.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (33336 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (14262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (14262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (14262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (14262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (14262 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (14262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (14262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000561.123.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (14262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (65402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (65402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2302.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (65402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1098.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (65402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (65402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (65402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (65402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000311.124.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (65402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (286722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3010.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (286722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4472.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (286722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (286722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12071.00 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (286722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3641.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (286722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4816.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (286722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10092.61 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000021.125.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (286722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 292.72 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000471.126.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1173.66 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (93508 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3936.69 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (93508 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 374.03 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (93508 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1570.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (93508 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3291.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (93508 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (93508 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (93508 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1187.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000221.127.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (93508 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (66572 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (66572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-08 22.6 1.0 2e-08 21.9 1.0 1.2 0 frame_4 Domain annotation for each sequence: >> frame_4 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (66572 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 934.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (66572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (66572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2343.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (66572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1038.52 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (66572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000301.128.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (66572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (384744 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6002.01 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (384744 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1538.98 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (384744 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 16197.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (384744 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4039.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (384744 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6463.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (384744 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1000.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (384744 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4886.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000081.12.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (384744 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 13542.99 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (42180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (42180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (42180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (42180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (42180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (42180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 109.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (42180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000411.129.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (42180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (148342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5221.64 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (148342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (148342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2492.15 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (148342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6245.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (148342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (148342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (148342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000121.130.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (148342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (55892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (55892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (55892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (55892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (55892 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (55892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (55892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000371.131.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (55892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (213700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (213700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (213700 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 1666.86 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (213700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8996.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (213700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (213700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3590.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (213700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000061.132.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (213700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6096 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6096 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6096 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6096 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6096 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6096 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6096 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000671.133.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6096 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (189588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (189588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 758.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (189588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3185.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (189588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (189588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2407.77 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (189588 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-07 18.1 0.6 4.6e-07 17.5 0.6 1.1 0 frame_3 Domain annotation for each sequence: >> frame_3 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (189588 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.09u 0.01s 00:00:00.10 Elapsed: 00:00:00.10 # Mc/sec: 798.17 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000091.134.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (189588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6673.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (60492 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 241.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (60492 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1016.27 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (60492 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (60492 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (60492 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2546.71 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (60492 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (60492 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 635.17 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000331.135.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (60492 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (17954 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (17954 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (17954 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 71.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (17954 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (17954 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (17954 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (17954 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000511.136.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (17954 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (182068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (182068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (182068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6408.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (182068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1911.71 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (182068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 473.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (182068 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2840.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (182068 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2312.26 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000101.137.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (182068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7665.06 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (15694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (15694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (15694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (15694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (15694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (15694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (15694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000541.138.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (15694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 199.31 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (37034 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (37034 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (37034 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (37034 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (37034 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1559.13 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (37034 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (37034 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000251.13.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (37034 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (309548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 5200.41 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (309548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10896.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (309548 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 2414.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (309548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 13031.97 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (309548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3250.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (309548 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 804.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (309548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000011.139.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (309548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1238.19 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (213432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (213432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 7512.81 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (213432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8985.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (213432 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3329.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (213432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 853.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (213432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (213432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000071.140.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (213432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (224312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3499.27 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (224312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9443.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (224312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (224312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3768.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (224312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2848.76 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (224312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (224312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000051.141.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (224312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7895.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (42208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 443.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (42208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (42208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (42208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (42208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 109.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (42208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1776.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (42208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000401.142.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (42208 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (59686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (59686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (59686 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2512.78 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (59686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (59686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 238.74 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (59686 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (59686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000341.143.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (59686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 758.01 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (286242 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (286242 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4808.87 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (286242 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3005.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (286242 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4465.38 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (286242 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (286242 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10075.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (286242 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000031.144.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (286242 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12050.79 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (59482 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2093.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (59482 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 999.30 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (59482 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 154.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (59482 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (59482 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (59482 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (59482 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000351.145.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (59482 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (8734 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 34.94 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (8734 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (8734 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 22.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (8734 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (8734 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 136.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (8734 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (8734 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000631.146.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (8734 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 367.70 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (9144 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (9144 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (9144 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (9144 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (9144 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 384.96 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (9144 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (9144 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000611.147.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (9144 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 153.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (107290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (107290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1362.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (107290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (107290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1802.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (107290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4516.91 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (107290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1126.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (107290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1673.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000191.148.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (107290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (116920 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (116920 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4922.33 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (116920 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (116920 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (116920 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (116920 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1484.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (116920 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000151.14.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (116920 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1964.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (101140 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (101140 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (101140 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1577.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (101140 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3560.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (101140 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (101140 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 262.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (101140 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1284.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000211.149.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (101140 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1061.97 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (204556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3436.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (204556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2147.84 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (204556 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3191.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (204556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 531.85 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (204556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (204556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (204556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8611.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000081.150.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (204556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (112380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3955.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (112380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (112380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (112380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1753.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (112380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4731.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (112380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1179.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (112380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1427.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000171.151.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (112380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 449.52 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (85994 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3620.35 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (85994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3026.99 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (85994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (85994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1444.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (85994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (85994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (85994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000231.152.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (85994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1092.12 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (8214 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 86.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (8214 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (8214 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (8214 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (8214 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (8214 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (8214 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 21.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000641.153.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (8214 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 345.81 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (23080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 812.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (23080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (23080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (23080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (23080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (23080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 293.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (23080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 387.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000491.154.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (23080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (61578 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 960.62 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (61578 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (61578 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (61578 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (61578 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 246.31 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (61578 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (61578 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000321.155.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-10 28.0 0.2 4.9e-10 27.3 0.2 1.2 1 frame_4 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 27.3 0.2 8.1e-11 4.9e-10 62 150 .. 6919 7012 .. 6902 7023 .. 0.79 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (61578 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 518.49 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (83294 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 216.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (83294 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 333.18 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (83294 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2931.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (83294 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3506.68 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (83294 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (83294 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (83294 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000261.156.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (83294 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 63.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000681.157.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (16246 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (16246 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 272.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (16246 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (16246 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 170.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (16246 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (16246 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (16246 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 64.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000531.158.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (16246 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 253.44 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (176978 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 1380.43 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (176978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (176978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (176978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (176978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (176978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2973.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (176978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000121.15.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (176978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (9082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 115.34 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (9082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (9082 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (9082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (9082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (9082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (9082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000621.159.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (9082 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (41344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 525.07 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (41344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (41344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (41344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (41344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (41344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 644.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (41344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000421.160.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (41344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 694.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (113950 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 296.27 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (113950 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 455.80 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (113950 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (113950 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (113950 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1914.36 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (113950 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (113950 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1447.16 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000141.161.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (113950 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4797.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (24538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (24538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 863.74 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (24538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (24538 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 382.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (24538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 98.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (24538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (24538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000481.162.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (24538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (13122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (13122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (13122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (13122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (13122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (13122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (13122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000571.163.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (13122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (37478 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (37478 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (37478 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (37478 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1577.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (37478 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (37478 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (37478 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000441.164.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (37478 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (112528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4737.43 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (112528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (112528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (112528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1890.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (112528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (112528 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1755.44 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (112528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000161.165.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (112528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (103262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3634.82 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (103262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (103262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (103262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (103262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (103262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (103262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000201.166.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (103262 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (38570 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (38570 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 404.99 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (38570 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (38570 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (38570 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (38570 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1357.66 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (38570 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 489.84 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000431.167.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (38570 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (17606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 619.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (17606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (17606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (17606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (17606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (17606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (17606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000521.168.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (17606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (213168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (213168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 554.24 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (213168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (213168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8974.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (213168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (213168 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 1662.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (213168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000111.16.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (213168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 188.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000591.169.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (79362 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3341.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (79362 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 206.34 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (79362 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1007.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (79362 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 317.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (79362 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (79362 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (79362 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000291.170.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (79362 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (9846 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (9846 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (9846 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (9846 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (9846 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (9846 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (9846 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000601.171.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (9846 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (21510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (21510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (21510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (21510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 225.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (21510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 55.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (21510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 335.56 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (21510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000501.172.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (21510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 86.04 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (80222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 208.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (80222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 842.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (80222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1018.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (80222 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (80222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (80222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (80222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000271.173.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (80222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2823.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (35016 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (35016 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (35016 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (35016 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (35016 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (35016 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (35016 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 140.06 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000461.174.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (35016 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (141470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (141470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2376.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (141470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 565.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (141470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2206.93 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (141470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 367.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (141470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (141470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5955.89 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000131.175.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (141470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6352 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6352 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6352 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6352 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6352 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 267.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6352 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6352 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 66.70 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000661.176.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6352 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 223.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (37458 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 475.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (37458 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (37458 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 97.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (37458 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (37458 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (37458 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (37458 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000451.177.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (37458 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (245750 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3833.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (245750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8650.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (245750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2580.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (245750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10346.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (245750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4128.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (245750 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 983.00 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (245750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 638.95 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000041.178.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (245750 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3121.03 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (72602 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (72602 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (72602 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 290.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (72602 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 922.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (72602 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (72602 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2555.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (72602 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000221.17.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (72602 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3056.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (57280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (57280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (57280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (57280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (57280 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (57280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (57280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000361.179.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (57280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (12604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (12604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (12604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (12604 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (12604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (12604 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 196.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (12604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 443.66 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000581.180.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (12604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 530.63 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (46988 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (46988 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1653.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (46988 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 596.75 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (46988 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (46988 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (46988 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (46988 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 493.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000391.181.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (46988 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1978.19 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (84168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (84168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (84168 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1313.02 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (84168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (84168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (84168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (84168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000251.182.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (84168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (79978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1343.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (79978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 207.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (79978 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1247.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (79978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3367.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (79978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2815.23 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (79978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 319.91 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (79978 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 839.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000281.183.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (79978 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (85222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (85222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (85222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (85222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (85222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (85222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (85222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 894.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000241.184.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (85222 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 230.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 275.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000651.185.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (55116 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 925.95 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (55116 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (55116 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (55116 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (55116 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (55116 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (55116 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1940.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000381.186.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (55116 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (109898 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (109898 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1395.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (109898 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1846.29 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (109898 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3868.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (109898 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (109898 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (109898 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000181.187.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (109898 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (113700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (113700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1193.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (113700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1910.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (113700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (113700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (113700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1443.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (113700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000151.188.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (113700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4002.24 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (115384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (115384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (115384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4061.52 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (115384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (115384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4857.67 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (115384 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1799.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (115384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 300.00 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000161.18.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (115384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (157268 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (157268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6620.98 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-16 47.9 0.0 8.7e-16 47.2 0.0 1.4 1 frame_4 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 47.2 0.0 1.4e-16 8.7e-16 1 168 [] 3937 4092 .. 3937 4092 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (157268 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 660.53 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (157268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5535.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (157268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (157268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (157268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 408.90 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (157268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000111.189.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (14422 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (14422 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (14422 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (14422 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (14422 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (14422 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 151.43 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (14422 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 57.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLY010000551.190.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (14422 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (15840 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (15840 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (15840 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 247.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (15840 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (15840 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (15840 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (15840 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000601.191.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (15840 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (18292 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (18292 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (18292 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (18292 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 643.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (18292 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (18292 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (18292 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 770.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000581.192.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (18292 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (7064 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (7064 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (7064 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (7064 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (7064 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (7064 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (7064 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000741.193.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (7064 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (69342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (69342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (69342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1164.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (69342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (69342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (69342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 277.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (69342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000241.194.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (69342 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (7952 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (7952 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (7952 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (7952 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (7952 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (7952 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (7952 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000701.195.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (7952 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (54660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1924.03 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (54660 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (54660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 218.64 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (54660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2301.19 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (54660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 573.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (54660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (54660 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 852.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000351.196.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (54660 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6774 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6774 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 238.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6774 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 27.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000751.197.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 17.61 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (63134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 801.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (63134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1060.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (63134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (63134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2657.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (63134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (63134 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (63134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000291.198.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (63134 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1159290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 13602.34 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1159290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7361.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1159290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9738.04 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1159290 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9042.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1159290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12172.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1159290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 16268.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1159290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4637.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NC_0178601.1.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1159290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3014.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (99880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4204.95 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (99880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (99880 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1558.13 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (99880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1268.48 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (99880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (99880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1677.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (99880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3515.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000191.19.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (99880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (20958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (20958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (20958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (20958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (20958 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (20958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 83.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (20958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000561.199.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (20958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (97848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 254.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (97848 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 2059.70 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (97848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (97848 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (97848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (97848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (97848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000181.200.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (97848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (51368 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 133.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (51368 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (51368 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 652.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (51368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 539.36 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (51368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (51368 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (51368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000381.201.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (51368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 862.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (19154 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (19154 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (19154 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (19154 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (19154 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (19154 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 321.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (19154 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000571.202.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (19154 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (130106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2185.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (130106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 5477.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (130106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1366.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (130106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (130106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 338.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (130106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (130106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 520.42 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000111.203.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (130106 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (32130 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (32130 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (32130 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (32130 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 337.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (32130 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 501.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (32130 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1352.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (32130 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000451.204.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (32130 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (55142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (55142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (55142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (55142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (55142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (55142 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (55142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 143.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000341.205.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (55142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (55656 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (55656 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (55656 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (55656 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2343.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (55656 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (55656 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (55656 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000331.206.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (55656 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (25518 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 102.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (25518 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 324.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (25518 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (25518 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 898.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (25518 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 428.70 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (25518 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (25518 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000511.207.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (25518 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 398.08 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (12904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (12904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (12904 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (12904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 216.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (12904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (12904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (12904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 454.22 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000661.208.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (12904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (413068 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 536.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (413068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 17390.16 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (413068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 5245.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (413068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (413068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4337.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (413068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6939.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (413068 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 3221.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000071.20.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (413068 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (101808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (101808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3583.64 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (101808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (101808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (101808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (101808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (101808 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1292.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000141.209.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (101808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (73268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2579.03 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (73268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (73268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 930.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (73268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1230.90 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (73268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1142.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (73268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (73268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000221.210.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (73268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (82168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (82168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (82168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (82168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3459.27 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (82168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (82168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (82168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000201.211.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (82168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (66460 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (66460 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (66460 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (66460 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (66460 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (66460 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (66460 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000251.212.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (66460 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 697.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (210956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7425.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (210956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3290.91 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (210956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (210956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (210956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8881.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (210956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (210956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2215.04 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000071.213.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (210956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3544.06 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (72374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 188.17 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (72374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 759.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (72374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2547.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (72374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (72374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 289.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (72374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (72374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3046.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000231.214.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (72374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (9254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (9254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (9254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 97.17 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (9254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (9254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (9254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (9254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000681.215.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (9254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (179166 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6306.64 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (179166 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2794.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (179166 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (179166 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (179166 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2275.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (179166 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (179166 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7542.89 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000081.216.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (179166 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3009.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (252320 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1009.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (252320 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8881.66 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (252320 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (252320 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2649.36 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (252320 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10622.67 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (252320 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (252320 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000051.217.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (252320 residues searched) Passed MSV filter: 4 (0.666667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 1968.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (39150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (39150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (39150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (39150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (39150 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 610.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (39150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 156.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (39150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000421.218.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (39150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (63318 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (63318 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (63318 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 164.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (63318 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (63318 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (63318 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 253.27 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (63318 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000231.21.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (63318 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 804.14 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (102814 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (102814 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1079.55 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (102814 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1603.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (102814 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (102814 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (102814 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 267.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (102814 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000131.219.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (102814 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4328.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (15930 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 41.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (15930 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (15930 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (15930 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (15930 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (15930 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (15930 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 248.51 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000591.220.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (15930 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (307290 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 2396.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (307290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1229.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (307290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10816.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (307290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-15 46.0 0.0 3.2e-15 45.3 0.0 1.4 1 frame_6 Domain annotation for each sequence: >> frame_6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 45.3 0.0 5.4e-16 3.2e-15 1 168 [] 32177 32332 .. 32177 32332 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (307290 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.11u 0.01s 00:00:00.12 Elapsed: 00:00:00.10 # Mc/sec: 516.25 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (307290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (307290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6468.45 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (307290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000021.221.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (30960 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1089.79 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (30960 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (30960 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (30960 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (30960 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (30960 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 80.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (30960 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 520.13 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000461.222.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-09 24.2 0.8 6.5e-09 23.6 0.8 1.1 0 frame_1 Domain annotation for each sequence: >> frame_1 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (30960 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 651.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (7732 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (7732 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 81.19 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (7732 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (7732 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (7732 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (7732 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (7732 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000711.223.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (7732 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (143254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (143254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (143254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2406.67 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (143254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6030.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (143254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (143254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (143254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1819.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000091.224.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (143254 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (15152 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (15152 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 60.61 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (15152 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (15152 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (15152 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (15152 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (15152 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000621.225.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (15152 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 637.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (140526 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 365.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (140526 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5916.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (140526 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (140526 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (140526 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4946.52 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (140526 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2192.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (140526 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000101.226.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (140526 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (23042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 292.63 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (23042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (23042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (23042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (23042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (23042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (23042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 970.07 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000531.227.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (23042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (52386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (52386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (52386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (52386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 209.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (52386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 880.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (52386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (52386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000361.228.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (52386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2205.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (112538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (112538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (112538 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (112538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (112538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3961.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (112538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (112538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1181.65 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000171.22.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (112538 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (100368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (100368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1565.74 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (100368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (100368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (100368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1053.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (100368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (100368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3532.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000161.229.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (100368 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (99108 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (99108 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (99108 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1546.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (99108 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (99108 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3488.60 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (99108 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1040.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (99108 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000171.230.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (99108 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4172.45 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (42100 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 656.76 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (42100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 707.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (42100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (42100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (42100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (42100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1772.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (42100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000411.231.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (42100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (22080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 929.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (22080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (22080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (22080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (22080 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 57.41 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (22080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (22080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000551.232.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (22080 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (15374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (15374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 239.83 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (15374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 541.16 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (15374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (15374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 647.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (15374 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (15374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000611.233.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (15374 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 39.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (30060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (30060 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (30060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 315.63 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (30060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (30060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (30060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (30060 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000471.234.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (30060 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1058.11 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (10994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (10994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (10994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (10994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (10994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (10994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (10994 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 28.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000671.235.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (10994 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (48794 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1717.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (48794 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 761.19 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (48794 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 619.68 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (48794 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2054.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (48794 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 195.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (48794 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (48794 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000401.236.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (48794 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (7260 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (7260 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 305.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (7260 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 255.55 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (7260 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (7260 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (7260 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 113.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (7260 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000731.237.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (7260 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 76.23 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (28540 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (28540 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (28540 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (28540 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 479.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (28540 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (28540 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 362.46 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (28540 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000481.238.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (28540 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (554996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7048.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (554996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8657.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (554996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 9767.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (554996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9323.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (554996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1442.99 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (554996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2219.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (554996 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5827.46 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000011.23.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (554996 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 7788.44 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (285444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1141.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (285444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (285444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12017.19 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (285444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (285444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10047.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (285444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4795.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (285444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000031.239.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (285444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (66454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 843.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (66454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (66454 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2797.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (66454 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 697.77 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (66454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (66454 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (66454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000261.240.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (66454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (323018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4102.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (323018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3391.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (323018 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6799.53 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (323018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (323018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (323018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 839.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (323018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1292.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000011.241.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (323018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11370.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (7536 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (7536 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (7536 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (7536 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 117.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (7536 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (7536 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 126.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (7536 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000721.242.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (7536 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 317.27 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (8914 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (8914 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (8914 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (8914 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 113.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (8914 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (8914 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (8914 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000691.243.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (8914 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (78908 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 205.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (78908 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (78908 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2777.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-09 25.1 0.2 3.5e-09 24.5 0.2 1.1 0 frame_6 Domain annotation for each sequence: >> frame_6 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (78908 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.07 # Mc/sec: 474.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (78908 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (78908 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (78908 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000211.244.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (78908 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (92624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (92624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (92624 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 370.50 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (92624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 240.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (92624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (92624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (92624 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3260.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000191.245.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (92624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1444.93 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (13900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (13900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (13900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (13900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (13900 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (13900 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (13900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000651.246.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (13900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (100548 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1568.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (100548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1689.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (100548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (100548 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (100548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3539.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (100548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (100548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 402.19 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000151.247.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (100548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 72.48 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1173.66 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.03 # Mc/sec: 327.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000501.248.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (27878 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (198820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (198820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (198820 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3101.59 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (198820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2087.61 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (198820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3340.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (198820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6998.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (198820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000101.24.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (198820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (56900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (56900 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 887.64 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (56900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (56900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (56900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (56900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (56900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000321.249.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (56900 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (14142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (14142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 179.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (14142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (14142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (14142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (14142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (14142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000641.250.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (14142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (28468 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (28468 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (28468 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (28468 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 478.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (28468 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (28468 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 113.87 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (28468 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000491.251.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (28468 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (51528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (51528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1813.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (51528 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (51528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 865.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (51528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (51528 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (51528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000371.252.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (51528 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (59380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2090.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (59380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 997.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (59380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (59380 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (59380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (59380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (59380 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000311.253.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (59380 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (22490 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (22490 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (22490 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (22490 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (22490 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (22490 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (22490 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000541.254.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (22490 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (23226 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (23226 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (23226 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 362.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (23226 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (23226 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 977.81 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (23226 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (23226 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000521.255.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (23226 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 390.20 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (14326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 504.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (14326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (14326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 57.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (14326 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 223.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (14326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (14326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (14326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000631.256.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (14326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 181.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (62268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (62268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (62268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 249.07 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (62268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (62268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (62268 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (62268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000301.257.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (62268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (50822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1788.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (50822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (50822 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 853.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (50822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (50822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2139.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (50822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (50822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000391.258.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (50822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (7200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (7200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 91.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (7200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (7200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (7200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (7200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (7200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000481.25.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (7200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (124528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (124528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (124528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 323.77 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (124528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (124528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2092.07 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (124528 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5242.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (124528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000121.259.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (124528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1581.51 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (63936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2250.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (63936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 997.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (63936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 811.99 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (63936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (63936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (63936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (63936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000271.260.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (63936 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (237102 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 616.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (237102 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3983.31 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (237102 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 1849.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (237102 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (237102 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (237102 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3011.20 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (237102 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9981.99 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000061.261.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (237102 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (32402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (32402 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (32402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (32402 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (32402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (32402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (32402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000441.262.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (32402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (63700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2242.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (63700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (63700 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (63700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1070.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (63700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (63700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (63700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000281.263.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (63700 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (36546 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1286.42 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (36546 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (36546 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (36546 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (36546 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (36546 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (36546 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1538.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000431.264.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (36546 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (260862 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (260862 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9182.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (260862 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (260862 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (260862 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (260862 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10982.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (260862 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4382.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSLZ010000041.265.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (260862 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (32992 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 85.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (32992 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 514.68 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (32992 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (32992 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (32992 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (32992 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (32992 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000241.266.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (32992 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (68408 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (68408 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2879.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (68408 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 718.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (68408 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (68408 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (68408 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (68408 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000201.267.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (68408 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (16850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (16850 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (16850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (16850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (16850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (16850 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (16850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 43.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000301.268.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (16850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (126198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1968.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (126198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2120.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (126198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4442.17 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (126198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (126198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (126198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1325.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (126198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000141.26.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (126198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (120372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (120372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4237.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (120372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 481.49 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (120372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (120372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2022.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (120372 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1877.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (120372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000151.269.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (120372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1263.91 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (17446 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (17446 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (17446 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-10 28.2 0.8 3.9e-10 27.6 0.8 1.1 1 frame_2 6.1e-10 27.0 0.2 9.2e-10 26.4 0.2 1.1 1 frame_4 Domain annotation for each sequence: >> frame_2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 27.6 0.8 1.3e-10 3.9e-10 59 156 .. 2376 2480 .. 2369 2502 .. 0.83 >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 26.4 0.2 3.1e-10 9.2e-10 62 149 .. 1054 1146 .. 1037 1155 .. 0.79 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (17446 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 2 (0.333333); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 244.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (17446 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (17446 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (17446 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000291.270.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (17446 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (7112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (7112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (7112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (7112 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (7112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (7112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (7112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000371.271.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (7112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (8962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 113.82 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (8962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (8962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 315.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (8962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (8962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (8962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 150.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (8962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 377.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000351.272.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (8962 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 139.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (173680 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 694.72 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (173680 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (173680 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (173680 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (173680 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (173680 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 3655.96 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (173680 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2709.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000101.273.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (173680 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2205.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (180800 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (180800 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6364.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (180800 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (180800 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (180800 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (180800 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7611.68 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (180800 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000091.274.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (180800 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (34574 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 439.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (34574 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1455.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (34574 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 580.84 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (34574 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1217.00 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (34574 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (34574 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 539.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (34574 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000221.275.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (34574 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 138.30 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (39354 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (39354 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (39354 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (39354 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (39354 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1656.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (39354 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 499.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (39354 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000211.276.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (39354 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 661.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (803556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 1044.62 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (803556 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 2109.33 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (803556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03 # Mc/sec: 9428.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (803556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3214.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (803556 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 11276.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-14 42.6 0.0 3.8e-14 41.8 0.0 1.4 1 frame_1 Domain annotation for each sequence: >> frame_1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 41.8 0.0 6.3e-15 3.8e-14 1 168 [] 56561 56716 .. 56561 56716 .. 0.89 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (803556 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.20u 0.01s 00:00:00.21 Elapsed: 00:00:00.21 # Mc/sec: 642.84 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (803556 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10205.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (803556 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 4178.49 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000011.277.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (16090 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (16090 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (16090 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (16090 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (16090 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (16090 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (16090 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000311.278.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (16090 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (144298 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5079.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (144298 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (144298 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (144298 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (144298 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6074.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (144298 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (144298 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2424.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000121.27.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (144298 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1832.58 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (12494 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 209.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (12494 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (12494 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (12494 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 439.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (12494 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (12494 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (12494 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 131.19 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000331.279.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (12494 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 526.00 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (135756 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (135756 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1724.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (135756 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 352.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (135756 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5715.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (135756 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (135756 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1425.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (135756 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4778.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000131.280.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (135756 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2280.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (31326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (31326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (31326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (31326 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (31326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (31326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (31326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000251.281.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (31326 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (446964 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 9408.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (446964 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4693.12 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (446964 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6972.64 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (446964 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 15733.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (446964 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5676.44 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (446964 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1162.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (446964 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7509.00 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000041.282.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (446964 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1787.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (8646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 109.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (8646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (8646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (8646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 304.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (8646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 134.88 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (8646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (8646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000361.283.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (8646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (259568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 5463.91 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (259568 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4049.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (259568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 4568.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (259568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1038.27 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (259568 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 674.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (259568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4360.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (259568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000051.284.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (259568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2725.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (29654 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 311.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (29654 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 498.19 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (29654 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (29654 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 376.61 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (29654 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (29654 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (29654 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000271.285.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (29654 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (220084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (220084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 880.34 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (220084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3433.31 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (220084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (220084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (220084 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 4632.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (220084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000071.286.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (220084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7746.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (193822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (193822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6822.53 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (193822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (193822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 503.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (193822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (193822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (193822 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8159.91 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000081.287.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (193822 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3023.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (162712 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 650.85 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (162712 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (162712 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (162712 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (162712 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (162712 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6850.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (162712 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000111.288.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (162712 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (199552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (199552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3352.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (199552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 518.84 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (199552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (199552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (199552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-08 22.1 3.9 5e-07 17.4 0.9 2.2 0 frame_6 Domain annotation for each sequence: >> frame_6 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (199552 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.10u 0.01s 00:00:00.11 Elapsed: 00:00:00.10 # Mc/sec: 840.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000091.28.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (199552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (579750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2319.00 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (579750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7362.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (579750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (579750 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 4522.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (579750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 20407.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (579750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6087.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (579750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9739.80 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000031.289.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (579750 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 12203.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (134180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 536.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (134180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4723.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (134180 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2093.21 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (134180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 348.87 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (134180 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5648.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (134180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (134180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1704.09 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000141.290.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (134180 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2254.22 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (94710 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (94710 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (94710 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (94710 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3987.29 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (94710 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1202.82 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (94710 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (94710 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 246.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000181.291.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (94710 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (95270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1600.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (95270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 381.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (95270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (95270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3353.50 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (95270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (95270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (95270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000171.292.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (95270 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6238 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6238 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6238 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 97.31 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6238 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 65.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6238 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6238 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6238 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 104.80 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000381.293.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6238 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (31280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 328.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (31280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (31280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (31280 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (31280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (31280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (31280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000261.294.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (31280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (222198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3732.93 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (222198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (222198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 9354.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (222198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (222198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2333.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (222198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (222198 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3466.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000061.295.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (222198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (96682 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (96682 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 251.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (96682 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (96682 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (96682 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (96682 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3403.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (96682 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000161.296.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (96682 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1015.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (590142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6196.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (590142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7494.80 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (590142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1534.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (590142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2360.57 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-08 20.6 0.7 8.1e-08 20.0 0.7 1.2 0 frame_5 Domain annotation for each sequence: >> frame_5 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (590142 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.26u 0.01s 00:00:00.27 Elapsed: 00:00:00.27 # Mc/sec: 920.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (590142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10386.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (590142 residues searched) Passed MSV filter: 4 (0.666667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 2301.55 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000021.297.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (590142 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 3304.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6164 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6164 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 24.66 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6164 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6164 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6164 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6164 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6164 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000391.298.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6164 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 216.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (101760 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1587.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (101760 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (101760 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (101760 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 407.04 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (101760 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (101760 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (101760 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000181.2.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (101760 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (14350 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (14350 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (14350 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (14350 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (14350 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (14350 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 505.12 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (14350 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000401.29.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (14350 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (147752 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (147752 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 591.01 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (147752 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1876.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (147752 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (147752 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6220.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (147752 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (147752 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000121.299.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (147752 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (15736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 264.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (15736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 199.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (15736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (15736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (15736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (15736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (15736 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000321.300.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (15736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (22726 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 59.09 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (22726 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (22726 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (22726 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 381.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (22726 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 354.53 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (22726 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (22726 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000281.301.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (22726 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (93134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 242.15 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (93134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3920.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (93134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (93134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1452.89 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (93134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1564.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (93134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (93134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000191.302.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (93134 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1182.80 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (34386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (34386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (34386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (34386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (34386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (34386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (34386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000231.303.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (34386 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 188.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 48.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 31.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 202.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 126.59 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_NSMA010000341.304.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (12056 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4255048 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.28u 0.01s 00:00:00.29 Elapsed: 00:00:00.13 # Mc/sec: 13779.81 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4255048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 2765.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4255048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.10u 0.00s 00:00:00.10 Elapsed: 00:00:00.05 # Mc/sec: 29955.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4255048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 10807.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4255048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 4255.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-14 41.2 0.0 1.2e-13 40.2 0.0 1.6 1 frame_6 Domain annotation for each sequence: >> frame_6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 40.2 0.0 2e-14 1.2e-13 1 168 [] 253380 253535 .. 253380 253535 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4255048 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.81u 0.03s 00:00:00.84 Elapsed: 00:00:00.81 # Mc/sec: 882.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4255048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.05 # Mc/sec: 8935.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4255048 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.16u 0.02s 00:00:00.18 Elapsed: 00:00:00.10 # Mc/sec: 6637.87 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000011.305.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1647010 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 2141.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1647010 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6588.04 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1647010 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.04 # Mc/sec: 6423.34 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1647010 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 17334.78 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1647010 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 17293.60 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1647010 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 13834.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1647010 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 28987.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKN010000021.306.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1647010 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 20917.03 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1309748 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 5108.02 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1309748 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 15367.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1309748 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6876.18 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1309748 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 22003.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1309748 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5238.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1309748 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3405.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1309748 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 18380.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000021.307.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1309748 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 8316.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-36 112.5 0.0 2.9e-22 68.2 0.0 2.3 2 frame_5 4.4e-06 15.6 0.0 1.4e-05 14.0 0.0 1.8 0 frame_6 Domain annotation for each sequence: >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 68.2 0.0 9.7e-23 2.9e-22 1 168 [] 32666 32831 .. 32666 32831 .. 0.94 2 ! 42.1 0.0 1e-14 3e-14 1 168 [] 426262 426417 .. 426262 426417 .. 0.90 >> frame_6 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (3786660 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 2 (0.333333); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 1.44u 0.03s 00:00:01.47 Elapsed: 00:00:01.45 # Mc/sec: 438.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (3786660 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.21u 0.03s 00:00:00.24 Elapsed: 00:00:00.10 # Mc/sec: 5907.19 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (3786660 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.18u 0.02s 00:00:00.20 Elapsed: 00:00:00.15 # Mc/sec: 10627.89 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (3786660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.11u 0.01s 00:00:00.12 Elapsed: 00:00:00.06 # Mc/sec: 22215.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (3786660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 13253.31 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (3786660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 2461.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (3786660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 5048.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (3786660 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 12022.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1180.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000011.308.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (107820 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (107820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3795.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (107820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (107820 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (107820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1811.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (107820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4539.22 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (107820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000211.30.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (107820 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 431.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (619418 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 6519.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (619418 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 3633.92 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (619418 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10406.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (619418 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6503.89 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (619418 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7866.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (619418 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1610.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (619418 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2477.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000031.309.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (619418 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 3220.97 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (95300 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (95300 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 247.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (95300 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (95300 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4012.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (95300 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1210.31 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (95300 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (95300 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PEKM010000041.310.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (95300 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1000.65 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1357122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 11426.97 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1357122 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.05 # Mc/sec: 4234.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1357122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 15923.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1357122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7124.89 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1357122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5428.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1357122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8617.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1357122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 11399.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000021.311.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1357122 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3528.52 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (3807266 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.20u 0.02s 00:00:00.22 Elapsed: 00:00:00.15 # Mc/sec: 10685.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-14 41.6 0.0 9.9e-14 40.5 0.0 1.7 1 frame_3 Domain annotation for each sequence: >> frame_3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 40.5 0.0 1.7e-14 9.9e-14 1 168 [] 308204 308359 .. 308204 308359 .. 0.89 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (3807266 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.76u 0.02s 00:00:00.78 Elapsed: 00:00:00.74 # Mc/sec: 864.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (3807266 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.18u 0.03s 00:00:00.21 Elapsed: 00:00:00.12 # Mc/sec: 4949.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (3807266 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 7995.26 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (3807266 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05 # Mc/sec: 1979.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (3807266 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.11u 0.01s 00:00:00.12 Elapsed: 00:00:00.07 # Mc/sec: 19145.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (3807266 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 9670.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (3807266 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 5076.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1178.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000011.312.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (295746 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (295746 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3755.97 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (295746 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (295746 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12450.91 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (295746 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1182.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (295746 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4613.64 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (295746 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 768.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PESN010000031.313.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (295746 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4968.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-15 45.8 0.0 4e-15 45.0 0.0 1.4 1 frame_2 Domain annotation for each sequence: >> frame_2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 45.0 0.0 6.7e-16 4e-15 1 168 [] 415668 415823 .. 415668 415823 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (5555606 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 1.09u 0.03s 00:00:01.12 Elapsed: 00:00:01.05 # Mc/sec: 888.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (5555606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.06 # Mc/sec: 11759.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (5555606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 7407.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (5555606 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.29u 0.02s 00:00:00.31 Elapsed: 00:00:00.20 # Mc/sec: 11694.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (5555606 residues searched) Passed MSV filter: 4 (0.666667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.31u 0.04s 00:00:00.35 Elapsed: 00:00:00.16 # Mc/sec: 5416.72 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (5555606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 2888.92 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (5555606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.05 # Mc/sec: 11666.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (5555606 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.16u 0.01s 00:00:00.17 Elapsed: 00:00:00.09 # Mc/sec: 21728.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246961.314.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1178.67 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-22 68.3 0.0 4.3e-22 67.7 0.0 1.3 1 frame_1 1.3e-14 43.4 0.0 2e-14 42.7 0.0 1.3 1 frame_5 Domain annotation for each sequence: >> frame_1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 67.7 0.0 1.4e-22 4.3e-22 1 168 [] 865287 865452 .. 865287 865452 .. 0.94 >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 42.7 0.0 6.7e-15 2e-14 1 168 [] 370858 371013 .. 370858 371013 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (5521400 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 2 (0.333333); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 2.06u 0.05s 00:00:02.11 Elapsed: 00:00:01.08 # Mc/sec: 858.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (5521400 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.22u 0.02s 00:00:00.24 Elapsed: 00:00:00.15 # Mc/sec: 5742.26 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (5521400 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.06 # Mc/sec: 11686.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (5521400 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 3680.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (5521400 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.08 # Mc/sec: 24294.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (5521400 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 2871.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (5521400 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.30u 0.03s 00:00:00.32 Elapsed: 00:00:00.17 # Mc/sec: 13673.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (5521400 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.09u 0.01s 00:00:00.10 Elapsed: 00:00:00.07 # Mc/sec: 8282.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0246971.315.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1506360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 15816.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1506360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3916.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1506360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 17674.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1506360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 12653.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1506360 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 7833.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1506360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 21139.25 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1506360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 19130.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247281.316.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1506360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6025.44 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4023112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 4023.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4023112 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.24u 0.02s 00:00:00.26 Elapsed: 00:00:00.13 # Mc/sec: 13028.69 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4023112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 10218.70 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4023112 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.18u 0.03s 00:00:00.21 Elapsed: 00:00:00.10 # Mc/sec: 6276.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4023112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.12u 0.01s 00:00:00.13 Elapsed: 00:00:00.06 # Mc/sec: 23602.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4023112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 3486.70 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4023112 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 8448.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-14 41.6 0.0 7.1e-14 40.9 0.0 1.4 1 frame_6 Domain annotation for each sequence: >> frame_6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 40.9 0.0 1.2e-14 7.1e-14 1 168 [] 291231 291386 .. 291231 291386 .. 0.84 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4023112 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 1.20u 0.03s 00:00:01.23 Elapsed: 00:00:00.79 # Mc/sec: 855.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247271.317.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4128398 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.24u 0.01s 00:00:00.25 Elapsed: 00:00:00.14 # Mc/sec: 12414.68 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4128398 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 5366.92 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4128398 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.05 # Mc/sec: 8669.64 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-14 42.8 0.0 3.1e-14 42.1 0.0 1.4 1 frame_5 Domain annotation for each sequence: >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 42.1 0.0 5.1e-15 3.1e-14 1 168 [] 53585 53740 .. 53585 53740 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4128398 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.83u 0.02s 00:00:00.85 Elapsed: 00:00:00.83 # Mc/sec: 835.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4128398 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.26u 0.03s 00:00:00.29 Elapsed: 00:00:00.13 # Mc/sec: 4954.08 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4128398 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.11u 0.00s 00:00:00.11 Elapsed: 00:00:00.06 # Mc/sec: 24219.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4128398 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 4128.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4128398 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 17476.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1178.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247231.318.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (37572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (37572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (37572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (37572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (37572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (37572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (37572 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000301.31.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (37572 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1651694 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 1073.60 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1651694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 23178.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1651694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8671.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1651694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 19379.88 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1651694 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.07 # Mc/sec: 3680.92 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1651694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 3303.39 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1651694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10488.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247241.319.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1651694 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.01 # Mc/sec: 27748.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1366428 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10658.14 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1366428 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 5465.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1366428 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 19175.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1366428 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 1776.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1366428 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8676.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-23 70.4 0.0 1e-22 69.7 0.0 1.4 1 frame_2 Domain annotation for each sequence: >> frame_2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 69.7 0.0 1.7e-23 1e-22 1 168 [] 177798 177963 .. 177798 177963 .. 0.94 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1366428 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.30u 0.02s 00:00:00.32 Elapsed: 00:00:00.32 # Mc/sec: 717.37 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1366428 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 16032.76 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1366428 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7173.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247261.320.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4185230 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.05 # Mc/sec: 8788.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4185230 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 13288.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4185230 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 3348.18 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4185230 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 2720.40 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4185230 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.20u 0.03s 00:00:00.23 Elapsed: 00:00:00.12 # Mc/sec: 5440.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4185230 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.25u 0.02s 00:00:00.27 Elapsed: 00:00:00.14 # Mc/sec: 12585.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4185230 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.14u 0.00s 00:00:00.14 Elapsed: 00:00:00.07 # Mc/sec: 21045.73 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-18 56.2 0.0 1.1e-13 40.3 0.0 2.8 1 frame_1 Domain annotation for each sequence: >> frame_1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 40.3 0.0 1.9e-14 1.1e-13 1 168 [] 401239 401394 .. 401239 401394 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4185230 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.85u 0.02s 00:00:00.87 Elapsed: 00:00:00.81 # Mc/sec: 868.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247251.321.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1200344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 10106.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1200344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7622.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1200344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 10563.03 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1200344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 2400.69 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1200344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12603.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1200344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10082.89 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1200344 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 1560.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247301.322.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1200344 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 3745.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-14 42.4 0.0 3.9e-14 41.8 0.0 1.3 1 frame_1 1.2e-05 14.2 0.0 3.4e-05 12.7 0.0 1.7 0 frame_3 Domain annotation for each sequence: >> frame_1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 41.8 0.0 1.3e-14 3.9e-14 1 168 [] 80510 80665 .. 80510 80665 .. 0.84 >> frame_3 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4273872 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 2 (0.333333); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 1.71u 0.05s 00:00:01.76 Elapsed: 00:00:00.90 # Mc/sec: 797.79 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4273872 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 2778.02 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4273872 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 13569.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4273872 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 8547.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4273872 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 14958.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4273872 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.17u 0.02s 00:00:00.19 Elapsed: 00:00:00.10 # Mc/sec: 6667.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4273872 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.23u 0.02s 00:00:00.25 Elapsed: 00:00:00.15 # Mc/sec: 11995.33 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4273872 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.11u 0.02s 00:00:00.13 Elapsed: 00:00:00.07 # Mc/sec: 21491.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1178.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247291.323.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1474812 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07 # Mc/sec: 8869.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1474812 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 12978.35 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1474812 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 2949.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1474812 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 4601.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1474812 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 6243.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1474812 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3834.51 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1474812 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7742.76 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247331.324.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1474812 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 12388.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4382098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.05 # Mc/sec: 11130.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4382098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 5842.80 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4382098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.06 # Mc/sec: 7668.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-14 43.1 0.0 2.6e-14 42.3 0.0 1.4 1 frame_4 5.6e-06 15.2 0.0 1.6e-05 13.8 0.0 1.7 0 frame_5 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 42.3 0.0 8.8e-15 2.6e-14 1 168 [] 240317 240472 .. 240317 240472 .. 0.90 >> frame_5 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4382098 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 2 (0.333333); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 1.69u 0.03s 00:00:01.72 Elapsed: 00:00:00.90 # Mc/sec: 817.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4382098 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.24u 0.02s 00:00:00.26 Elapsed: 00:00:00.18 # Mc/sec: 10249.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4382098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 2278.69 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4382098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.09u 0.00s 00:00:00.09 Elapsed: 00:00:00.05 # Mc/sec: 30849.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4382098 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.15u 0.02s 00:00:00.17 Elapsed: 00:00:00.10 # Mc/sec: 6836.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247321.325.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4427564 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.05 # Mc/sec: 11246.01 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4427564 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.13u 0.01s 00:00:00.14 Elapsed: 00:00:00.07 # Mc/sec: 22264.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4427564 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.05 # Mc/sec: 9297.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4427564 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.32u 0.02s 00:00:00.34 Elapsed: 00:00:00.16 # Mc/sec: 11650.03 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-14 42.5 0.0 3.9e-14 41.8 0.0 1.4 1 frame_5 Domain annotation for each sequence: >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 41.8 0.0 6.6e-15 3.9e-14 1 168 [] 80281 80436 .. 80281 80436 .. 0.84 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4427564 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.92u 0.03s 00:00:00.95 Elapsed: 00:00:00.87 # Mc/sec: 854.98 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4427564 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 2877.92 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4427564 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 4427.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4427564 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.14u 0.02s 00:00:00.16 Elapsed: 00:00:00.09 # Mc/sec: 7674.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1178.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247341.326.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1200110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 10560.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1200110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3120.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1200110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7620.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1200110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 10104.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1200110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 6720.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1200110 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 3744.34 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1200110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 2400.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0247351.327.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1200110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 6300.58 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4242206 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.13u 0.00s 00:00:00.13 Elapsed: 00:00:00.07 # Mc/sec: 21332.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4242206 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.22u 0.03s 00:00:00.25 Elapsed: 00:00:00.13 # Mc/sec: 13738.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4242206 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.13u 0.01s 00:00:00.14 Elapsed: 00:00:00.08 # Mc/sec: 8272.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-14 42.8 0.0 3.3e-14 42.0 0.0 1.4 1 frame_5 Domain annotation for each sequence: >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 42.0 0.0 5.5e-15 3.3e-14 1 168 [] 86918 87073 .. 86918 87073 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4242206 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.84u 0.01s 00:00:00.85 Elapsed: 00:00:00.84 # Mc/sec: 848.44 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4242206 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 8908.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4242206 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 5514.87 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4242206 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 8484.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4242206 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 17958.67 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000011.328.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (115276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1210.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (115276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 461.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (115276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 299.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (115276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1936.64 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (115276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (115276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4853.12 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (115276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000191.32.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (115276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1321552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8391.86 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1321552 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05 # Mc/sec: 4123.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1321552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11101.04 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1321552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3436.04 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1321552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6938.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1321552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 15506.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1321552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5286.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000021.329.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1321552 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 27818.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (33030 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (33030 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (33030 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (33030 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (33030 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 132.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (33030 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (33030 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PGGD010000031.330.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (33030 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4136212 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 4136.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4136212 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 8686.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-14 41.6 0.0 7.4e-14 40.9 0.0 1.4 1 frame_1 Domain annotation for each sequence: >> frame_1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 40.9 0.0 1.2e-14 7.4e-14 1 168 [] 454693 454848 .. 454693 454848 .. 0.84 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4136212 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 1.18u 0.04s 00:00:01.22 Elapsed: 00:00:00.76 # Mc/sec: 914.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4136212 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.12u 0.01s 00:00:00.13 Elapsed: 00:00:00.07 # Mc/sec: 20799.24 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4136212 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.06 # Mc/sec: 8754.98 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4136212 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 2688.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4136212 residues searched) Passed MSV filter: 4 (0.666667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.18u 0.03s 00:00:00.21 Elapsed: 00:00:00.11 # Mc/sec: 5865.90 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4136212 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.21u 0.02s 00:00:00.23 Elapsed: 00:00:00.15 # Mc/sec: 11608.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000011.331.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1919124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 3838.25 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-12 36.8 0.0 2.2e-12 36.1 0.0 1.3 1 frame_3 Domain annotation for each sequence: >> frame_3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 36.1 0.0 3.7e-13 2.2e-12 1 45 [. 313860 313905 .. 313860 313910 .. 0.94 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1919124 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.37u 0.01s 00:00:00.38 Elapsed: 00:00:00.37 # Mc/sec: 871.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1919124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 12186.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1919124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 4989.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1919124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.02 # Mc/sec: 40397.56 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1919124 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 7484.58 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1919124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 20150.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1919124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 22517.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40266 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40266 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1296.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENE010000021.332.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40266 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1159.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1474018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 17295.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1474018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7738.59 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1474018 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.06 # Mc/sec: 10342.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1474018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5896.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-27 84.6 0.3 5.4e-26 80.4 0.3 2.2 1 frame_5 5.5e-23 70.6 0.0 1.1e-22 69.6 0.0 1.5 1 frame_4 Domain annotation for each sequence: >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 80.4 0.3 1.8e-26 5.4e-26 1 168 [] 194788 194932 .. 194788 194932 .. 0.91 >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 69.6 0.0 3.7e-23 1.1e-22 1 168 [] 167549 167714 .. 167549 167714 .. 0.94 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1474018 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 2 (0.333333); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.55u 0.02s 00:00:00.57 Elapsed: 00:00:00.56 # Mc/sec: 442.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1474018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 11497.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1474018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9360.01 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1474018 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 1916.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40860 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1315.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40860 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000021.333.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40860 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (3987638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 13956.73 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (3987638 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.19u 0.02s 00:00:00.21 Elapsed: 00:00:00.14 # Mc/sec: 11991.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (3987638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 2591.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-15 44.1 0.0 1.4e-14 43.2 0.0 1.5 1 frame_1 Domain annotation for each sequence: >> frame_1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 43.2 0.0 2.4e-15 1.4e-14 1 168 [] 194832 194987 .. 194832 194987 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (3987638 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.78u 0.03s 00:00:00.81 Elapsed: 00:00:00.74 # Mc/sec: 905.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (3987638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 5316.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (3987638 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.16u 0.03s 00:00:00.19 Elapsed: 00:00:00.12 # Mc/sec: 5183.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (3987638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 12660.75 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (3987638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.08u 0.00s 00:00:00.08 Elapsed: 00:00:00.05 # Mc/sec: 28072.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENF010000011.334.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (618958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2475.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (618958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7860.77 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (618958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 13029.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-23 71.5 0.0 4.5e-23 70.9 0.0 1.3 1 frame_5 Domain annotation for each sequence: >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 70.9 0.0 7.5e-24 4.5e-23 1 168 [] 60988 61153 .. 60988 61153 .. 0.94 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (618958 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.14u 0.00s 00:00:00.14 Elapsed: 00:00:00.14 # Mc/sec: 742.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (618958 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 4827.87 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (618958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (618958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1609.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (618958 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 10893.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000031.335.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-07 20.1 0.1 3.8e-06 15.8 0.1 2.4 0 frame_2 Domain annotation for each sequence: >> frame_2 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (343168 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.12u 0.01s 00:00:00.13 Elapsed: 00:00:00.13 # Mc/sec: 443.48 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (343168 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 2676.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (343168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12079.51 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (343168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7223.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (343168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (343168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4358.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (343168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3603.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000041.336.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (343168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1467924 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 2935.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1467924 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 7633.20 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-23 70.3 0.0 1.1e-22 69.6 0.0 1.3 1 frame_5 Domain annotation for each sequence: >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 69.6 0.0 1.8e-23 1.1e-22 1 168 [] 90456 90621 .. 90456 90621 .. 0.94 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1467924 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.27u 0.01s 00:00:00.28 Elapsed: 00:00:00.28 # Mc/sec: 880.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1467924 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 12917.73 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1467924 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7706.60 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1467924 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 12359.92 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1467924 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 6214.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1467924 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 1272.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000021.337.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1180.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (3312170 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 2152.91 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (3312170 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.26u 0.02s 00:00:00.28 Elapsed: 00:00:00.13 # Mc/sec: 10726.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-15 44.0 0.0 1.4e-14 43.2 0.0 1.4 1 frame_3 Domain annotation for each sequence: >> frame_3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 43.2 0.0 2.3e-15 1.4e-14 1 168 [] 251946 252101 .. 251946 252101 .. 0.91 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (3312170 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.65u 0.02s 00:00:00.67 Elapsed: 00:00:00.63 # Mc/sec: 883.25 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (3312170 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 4416.23 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (3312170 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 11592.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-42 131.9 6.2 9e-42 131.5 6.2 1.2 1 frame_4 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 131.5 6.2 1.5e-42 9e-42 3 352 .] 98605 98965 .. 98603 98965 .. 0.87 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (3312170 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 1.16u 0.03s 00:00:01.19 Elapsed: 00:00:01.13 # Mc/sec: 1022.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (3312170 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 10516.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (3312170 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.12u 0.01s 00:00:00.13 Elapsed: 00:00:00.09 # Mc/sec: 5741.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/lanl.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.lanl.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: lanl [M=55] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (55 nodes) Target sequences: 6 (42156 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 231.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF04738.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF04738.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_N [M=650] Accession: PF04738.15 Description: Lantibiotic dehydratase, N terminus Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-146 475.2 0.0 9.4e-146 475.0 0.0 1.1 1 AOIprotein6 Domain annotation for each sequence: >> AOIprotein6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 475.0 0.0 1.6e-146 9.4e-146 2 647 .. 3772 4417 .. 3771 4420 .. 0.95 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (650 nodes) Target sequences: 6 (42156 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07 # Mc/sec: 391.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-56 179.1 0.0 6.4e-56 178.8 0.0 1.1 1 AOIprotein5 Domain annotation for each sequence: >> AOIprotein5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.8 0.0 1.1e-56 6.4e-56 1 287 [. 4476 4744 .. 4476 4745 .. 0.92 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (42156 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 404.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF13575.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF13575.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: DUF4135 [M=377] Accession: PF13575.8 Description: Domain of unknown function (DUF4135) Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (377 nodes) Target sequences: 6 (42156 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENH010000011.338.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (10906 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 183.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (10906 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 138.51 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (10906 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (10906 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (10906 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (10906 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (10906 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000431.33.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (10906 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4373880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 4373.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4373880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 13887.07 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4373880 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.28u 0.00s 00:00:00.28 Elapsed: 00:00:00.17 # Mc/sec: 10831.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4373880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.12u 0.01s 00:00:00.13 Elapsed: 00:00:00.07 # Mc/sec: 21994.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4373880 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.24u 0.01s 00:00:00.25 Elapsed: 00:00:00.14 # Mc/sec: 4873.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4373880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 2843.02 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-17 51.5 0.0 6.1e-14 41.1 0.0 3.0 1 frame_4 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 41.1 0.0 1e-14 6.1e-14 1 168 [] 640247 640402 .. 640247 640402 .. 0.88 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4373880 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.89u 0.03s 00:00:00.92 Elapsed: 00:00:00.87 # Mc/sec: 844.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4373880 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 9185.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000011.339.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (307788 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (307788 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5170.84 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (307788 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3231.77 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (307788 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (307788 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (307788 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6478.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (307788 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10834.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000031.340.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (307788 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4801.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-23 70.4 0.0 1e-22 69.7 0.0 1.3 1 frame_4 6.3e-23 70.4 0.0 1e-22 69.7 0.0 1.3 1 frame_1 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 69.7 0.0 3.3e-23 1e-22 1 168 [] 101144 101309 .. 101144 101309 .. 0.94 >> frame_1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 69.7 0.0 3.3e-23 1e-22 1 168 [] 181928 182093 .. 181928 182093 .. 0.94 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1352098 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 2 (0.333333); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.49u 0.02s 00:00:00.51 Elapsed: 00:00:00.50 # Mc/sec: 454.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1352098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 11898.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1352098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8585.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1352098 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 9487.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1352098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5408.39 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1352098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 1757.73 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1352098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10546.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1352098 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 14197.03 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1180.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_PENG010000021.341.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (4144012 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.18u 0.01s 00:00:00.19 Elapsed: 00:00:00.12 # Mc/sec: 14538.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-22 68.9 0.0 3.2e-22 68.1 0.0 1.4 1 frame_4 5.6e-14 41.3 0.0 9.7e-14 40.5 0.0 1.4 1 frame_2 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 68.1 0.0 1.1e-22 3.2e-22 1 168 [] 619947 620112 .. 619947 620112 .. 0.94 >> frame_2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 40.5 0.0 3.2e-14 9.7e-14 1 168 [] 204786 204941 .. 204786 204941 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (4144012 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 2 (0.333333); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 1.57u 0.04s 00:00:01.61 Elapsed: 00:00:00.80 # Mc/sec: 870.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (4144012 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.11u 0.01s 00:00:00.12 Elapsed: 00:00:00.07 # Mc/sec: 20838.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (4144012 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.04 # Mc/sec: 13157.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (4144012 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 5525.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (4144012 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 2693.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (4144012 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 8702.43 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (4144012 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.21u 0.02s 00:00:00.23 Elapsed: 00:00:00.12 # Mc/sec: 5387.22 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1180.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300941.342.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1754106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 15436.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-23 70.0 0.0 1.3e-22 69.4 0.0 1.4 1 frame_6 8.5e-23 70.0 0.0 1.3e-22 69.4 0.0 1.3 1 frame_3 Domain annotation for each sequence: >> frame_6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 69.4 0.0 4.4e-23 1.3e-22 1 168 [] 34041 34206 .. 34041 34206 .. 0.94 >> frame_3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 69.4 0.0 4.4e-23 1.3e-22 1 168 [] 120548 120713 .. 120548 120713 .. 0.94 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1754106 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 2 (0.333333); expected 0.0 (0.001) Passed Fwd filter: 2 (0.333333); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.71u 0.02s 00:00:00.73 Elapsed: 00:00:00.38 # Mc/sec: 775.50 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1754106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 3508.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1754106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 2280.34 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1754106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11138.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1754106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 13682.03 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1754106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9209.06 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1754106 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.05 # Mc/sec: 14769.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1319.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_CP0300951.343.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40986 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1533.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1651.27 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05 # Mc/sec: 827.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000191.344.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (65370 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (65370 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (65370 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (65370 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1019.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (65370 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (65370 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (65370 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000241.345.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (65370 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (48496 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (48496 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (48496 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 509.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (48496 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2041.68 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (48496 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 814.73 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (48496 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (48496 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 193.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000381.346.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (48496 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 756.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 67.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000391.347.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (123198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (123198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (123198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5186.64 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (123198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (123198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (123198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4336.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (123198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1564.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000151.348.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (123198 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (116312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (116312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (116312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (116312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1814.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (116312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4896.74 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (116312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (116312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000181.34.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (116312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1954.04 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 916.69 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 87.10 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000401.349.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (41624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (41624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1752.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (41624 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (41624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (41624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 437.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (41624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (41624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 649.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000321.350.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (41624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (92404 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (92404 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (92404 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (92404 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (92404 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3890.21 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (92404 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1552.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (92404 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 369.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000261.351.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (92404 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (106686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4491.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (106686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (106686 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1664.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (106686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 277.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (106686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (106686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1792.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (106686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 426.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000171.352.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (106686 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (10416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 162.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (10416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 174.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (10416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (10416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (10416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (10416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (10416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000431.353.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (10416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 41.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 975.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1167.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000371.354.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (35444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (35444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 450.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (35444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (35444 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 552.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (35444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (35444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (35444 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1247.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000341.355.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (35444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (357510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 7525.59 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (357510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 929.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (357510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3753.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (357510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12584.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (357510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1430.04 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (357510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (357510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6006.17 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000041.356.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (357510 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5577.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (86454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1452.43 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (86454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (86454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1348.68 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (86454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (86454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3639.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (86454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (86454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000211.357.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (86454 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2321.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6433.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7694.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 4 (0.666667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2851.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1919.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000091.358.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (13768 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (13768 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (13768 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (13768 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 231.30 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (13768 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (13768 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 55.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (13768 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000421.35.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (13768 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (132876 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2072.87 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (132876 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (132876 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (132876 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (132876 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1395.20 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (132876 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4677.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (132876 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000131.359.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (132876 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (661642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 13927.56 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (661642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8402.85 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (661642 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1720.27 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (661642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 23289.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-14 42.9 0.0 3.1e-14 42.1 0.0 1.4 1 frame_6 Domain annotation for each sequence: >> frame_6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 42.1 0.0 5.1e-15 3.1e-14 1 168 [] 54114 54269 .. 54114 54269 .. 0.89 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (661642 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.14u 0.00s 00:00:00.14 Elapsed: 00:00:00.15 # Mc/sec: 741.04 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (661642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6947.24 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (661642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2646.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (661642 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 3440.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000011.360.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2470.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1867.81 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 382.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6191.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1544.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2294.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000111.361.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (301106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5058.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (301106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4697.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (301106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3824.05 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (301106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (301106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3161.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (301106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12676.56 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (301106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10598.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000051.362.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (301106 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1204.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (198284 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3331.17 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (198284 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (198284 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 515.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (198284 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2081.98 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (198284 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (198284 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6979.60 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (198284 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8347.76 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000081.363.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (198284 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 792.25 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 598.91 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000301.364.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (246652 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2589.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (246652 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 5192.02 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (246652 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3847.77 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (246652 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8682.15 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (246652 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3132.48 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (246652 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 641.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (246652 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4143.75 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000071.365.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (246652 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 986.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (108740 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (108740 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (108740 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (108740 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (108740 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3827.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (108740 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1696.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (108740 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1141.77 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000201.366.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (108740 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (525922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (525922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2103.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (525922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6679.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (525922 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11070.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (525922 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 2945.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (525922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5522.18 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (525922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9256.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000031.367.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (525922 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8204.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 741.84 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 798.91 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2002.02 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000291.368.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 123.64 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (135528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1721.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (135528 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5705.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (135528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (135528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4770.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (135528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2276.87 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (135528 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (135528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 542.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000131.36.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (135528 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (173276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2200.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (173276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (173276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 693.10 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (173276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1819.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (173276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7294.92 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (173276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (173276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000101.369.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (173276 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (59042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 236.17 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (59042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 749.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (59042 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (59042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (59042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 991.91 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (59042 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2485.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (59042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 619.94 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000271.370.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (59042 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2078.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (41094 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (41094 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (41094 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1730.06 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (41094 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (41094 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (41094 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (41094 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 521.89 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000331.371.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (41094 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (124604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 323.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (124604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1582.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (124604 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1943.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (124604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (124604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (124604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (124604 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1308.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000141.372.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (124604 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4386.06 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1433.78 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1761.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1185.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3973.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000161.373.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (32392 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1140.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (32392 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (32392 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 505.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (32392 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (32392 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 411.38 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (32392 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (32392 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 544.19 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000351.374.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (32392 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (47104 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (47104 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1983.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (47104 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (47104 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1658.06 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (47104 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (47104 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (47104 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000311.375.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (47104 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 791.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000421.376.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (32770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (32770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (32770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 416.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (32770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1379.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (32770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1153.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (32770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (32770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000411.377.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (32770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (142770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2398.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (142770 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2227.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (142770 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1813.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (142770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (142770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 371.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (142770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (142770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6010.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000121.378.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (142770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5025.50 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (211856 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2690.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (211856 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3304.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (211856 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7457.33 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (211856 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (211856 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (211856 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 847.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (211856 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000081.37.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (211856 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (54582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 693.19 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (54582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (54582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (54582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (54582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2297.90 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (54582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (54582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000281.379.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (54582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1172.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000231.380.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (9706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (9706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (9706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (9706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (9706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (9706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (9706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000441.381.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (9706 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (284288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2985.02 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (284288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10006.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (284288 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 11968.52 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (284288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1137.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (284288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3610.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (284288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (284288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 739.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000061.382.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (284288 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 2217.45 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (106600 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1119.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (106600 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (106600 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (106600 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (106600 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1790.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (106600 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (106600 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 277.16 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000181.383.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (106600 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4487.86 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2845.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000221.384.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 323.39 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (61806 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (61806 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 648.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (61806 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (61806 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (61806 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (61806 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (61806 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000251.385.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (61806 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (33470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 133.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (33470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (33470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (33470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 351.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (33470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (33470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (33470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000361.386.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (33470 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (8530 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (8530 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (8530 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (8530 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (8530 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (8530 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (8530 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000481.387.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (8530 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (428384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1713.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (428384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6682.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (428384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5440.48 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (428384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4498.03 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (428384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1113.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (428384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 18034.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (428384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7196.85 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEM010000021.388.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (428384 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 15079.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-08 20.6 1.0 8e-08 20.0 1.0 1.1 0 frame_3 Domain annotation for each sequence: >> frame_3 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (253892 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.16u 0.00s 00:00:00.16 Elapsed: 00:00:00.17 # Mc/sec: 628.76 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (253892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4265.39 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (253892 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 660.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (253892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2665.87 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (253892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (253892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8937.00 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (253892 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1015.57 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000051.38.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (253892 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3960.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (33588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 352.67 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (33588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 426.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (33588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (33588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 564.28 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (33588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 87.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (33588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (33588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1414.05 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000361.389.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (33588 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (86448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3042.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (86448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (86448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (86448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (86448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (86448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (86448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1452.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000201.390.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (86448 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1348.59 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (20832 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (20832 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 264.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (20832 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (20832 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (20832 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (20832 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (20832 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000431.391.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (20832 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (132888 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (132888 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (132888 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1687.68 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (132888 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5594.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (132888 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2073.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (132888 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (132888 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000131.392.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (132888 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4677.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (123176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (123176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (123176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (123176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2069.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (123176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5185.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (123176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1564.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (123176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4335.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000161.393.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (123176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (661504 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11642.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (661504 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8401.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (661504 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2646.02 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-14 42.9 0.0 3.1e-14 42.1 0.0 1.4 1 frame_5 Domain annotation for each sequence: >> frame_5 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 42.1 0.0 5.1e-15 3.1e-14 1 168 [] 54118 54273 .. 54118 54273 .. 0.89 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (661504 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.17u 0.01s 00:00:00.18 Elapsed: 00:00:00.17 # Mc/sec: 653.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (661504 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 859.96 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (661504 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6945.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (661504 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 5159.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (661504 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 13924.66 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000011.394.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (284576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10017.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (284576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3614.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (284576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4780.88 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (284576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (284576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (284576 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (284576 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03 # Mc/sec: 3993.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000071.395.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (284576 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 2219.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (125046 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (125046 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (125046 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1312.98 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (125046 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4401.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (125046 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 325.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (125046 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (125046 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000141.396.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (125046 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2100.77 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (198188 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2080.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (198188 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8343.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (198188 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 792.75 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (198188 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (198188 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (198188 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (198188 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3329.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000081.397.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (198188 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 515.29 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (144150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (144150 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1830.70 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (144150 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (144150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (144150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1513.58 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (144150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (144150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6068.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000121.398.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (144150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (292248 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4909.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (292248 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (292248 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3068.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (292248 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4559.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (292248 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6151.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (292248 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1168.99 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (292248 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125931.3.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (292248 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10287.13 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (47638 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 743.15 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (47638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (47638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (47638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (47638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (47638 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (47638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000291.39.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (47638 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 110.90 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 352.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 975.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 432.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 291.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000371.399.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (27724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (61808 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 964.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (61808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (61808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (61808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (61808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (61808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (61808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000251.400.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (61808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 648.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6433.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7694.70 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 4 (0.666667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 2851.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000091.401.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (182772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2321.20 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 276.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 228.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 916.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 365.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 766.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000391.402.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (21774 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 339.67 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 910.06 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 328.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000381.403.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (25854 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 67.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1985.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 792.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 188.63 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000311.404.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (47158 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 495.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1651.27 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1533.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 393.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3459.81 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000191.405.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (98290 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 827.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1261.23 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3403.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 323.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000221.406.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (80848 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2845.85 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (106684 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (106684 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (106684 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (106684 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (106684 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 426.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (106684 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (106684 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000171.407.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (106684 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 4752.92 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1761.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1433.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000151.408.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (112896 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1896.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (7372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (7372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (7372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (7372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (7372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (7372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (7372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000461.40.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (7372 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (301100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5058.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (301100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (301100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (301100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 782.86 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (301100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3161.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (301100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12676.31 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (301100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4697.16 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000051.409.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (301100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (50174 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (50174 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (50174 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (50174 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (50174 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (50174 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (50174 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1766.12 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000281.410.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (50174 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (35314 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (35314 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (35314 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 370.80 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (35314 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (35314 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1486.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (35314 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (35314 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 448.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000341.411.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (35314 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 550.90 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1673.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 499.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2002.02 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 741.84 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000291.412.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (47554 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (32762 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (32762 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (32762 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (32762 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (32762 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (32762 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (32762 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1379.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000401.413.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (32762 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 511.09 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (32394 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (32394 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1363.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (32394 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 544.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (32394 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (32394 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (32394 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (32394 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000351.414.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (32394 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 129.58 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (91956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (91956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 239.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (91956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (91956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3236.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (91956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (91956 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (91956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000211.415.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (91956 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (47282 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 189.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (47282 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (47282 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (47282 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (47282 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 737.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (47282 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1664.33 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (47282 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000301.416.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (47282 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (428168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (428168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (428168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 15071.51 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (428168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 9012.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (428168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7193.22 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (428168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (428168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000031.417.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (428168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (41642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (41642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (41642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (41642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (41642 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (41642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (41642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000321.418.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (41642 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (122100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (122100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (122100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (122100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2051.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (122100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 488.40 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (122100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (122100 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000151.41.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (122100 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5140.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (173280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 450.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (173280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2200.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (173280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 693.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (173280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7295.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (173280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2911.10 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (173280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (173280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6099.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000101.419.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (173280 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1819.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (105698 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1342.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (105698 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (105698 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 422.79 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (105698 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3720.57 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (105698 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (105698 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (105698 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000181.420.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (105698 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (65548 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1022.55 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (65548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (65548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2307.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (65548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (65548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (65548 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 262.19 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (65548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000241.421.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (65548 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (246702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3848.55 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (246702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (246702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2590.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (246702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8683.91 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (246702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (246702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 641.43 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (246702 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10386.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000061.422.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (246702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4144.59 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2457.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 732.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1172.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000231.423.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (69808 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 181.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 171.02 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 685.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000421.424.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (16288 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 573.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (20500 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 344.40 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (20500 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 53.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (20500 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (20500 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (20500 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (20500 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (20500 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 319.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000411.425.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (20500 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (59024 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (59024 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (59024 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2077.64 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (59024 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2484.91 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (59024 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (59024 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (59024 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000261.426.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (59024 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (40858 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (40858 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (40858 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (40858 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (40858 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (40858 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (40858 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000331.427.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (40858 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 518.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (57186 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (57186 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2012.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (57186 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2407.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (57186 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (57186 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 892.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (57186 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (57186 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 726.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000271.428.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (57186 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (7270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (7270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (7270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (7270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (7270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (7270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (7270 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000471.42.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (7270 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2470.81 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1544.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6191.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 588.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 382.39 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000111.429.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (147072 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (617962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10876.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (617962 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 3213.40 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (617962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2471.85 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (617962 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 3460.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (617962 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 6504.05 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (617962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1606.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (617962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6488.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000021.430.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (617962 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7848.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (357450 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7524.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (357450 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5576.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (357450 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12582.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (357450 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3753.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (357450 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1429.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (357450 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 929.37 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (357450 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_QXEN010000041.431.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (357450 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4539.61 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (1339414 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 11786.84 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (1339414 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 11277.87 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (1339414 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 7500.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (1339414 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5357.66 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (1339414 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7031.92 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (1339414 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 17010.56 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (1339414 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 5223.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000021.432.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (1339414 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 3482.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-14 42.4 0.0 3.8e-14 41.8 0.0 1.3 1 frame_4 Domain annotation for each sequence: >> frame_4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 41.8 0.0 6.3e-15 3.8e-14 1 168 [] 2069 2224 .. 2069 2224 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (3874904 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.74u 0.02s 00:00:00.76 Elapsed: 00:00:00.72 # Mc/sec: 904.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (3874904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.11u 0.01s 00:00:00.12 Elapsed: 00:00:00.07 # Mc/sec: 19485.23 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (3874904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 5166.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (3874904 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.15u 0.03s 00:00:00.18 Elapsed: 00:00:00.10 # Mc/sec: 6044.85 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (3874904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 10171.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (3874904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.03 # Mc/sec: 16403.76 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (3874904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 5037.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (3874904 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.24u 0.02s 00:00:00.26 Elapsed: 00:00:00.14 # Mc/sec: 11652.39 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (33336 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (33336 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1073.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_UGTO010000011.433.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (33336 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (478754 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (478754 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (478754 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 2489.52 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (478754 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5026.92 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (478754 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6080.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (478754 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8426.07 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-15 46.1 0.0 3.5e-15 45.2 0.0 1.5 1 frame_1 Domain annotation for each sequence: >> frame_1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 45.2 0.0 5.8e-16 3.5e-15 1 168 [] 10013 10168 .. 10013 10168 .. 0.90 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (478754 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.13u 0.01s 00:00:00.14 Elapsed: 00:00:00.14 # Mc/sec: 574.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (478754 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10077.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02624.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.PF02624.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: YcaO [M=322] Accession: PF02624.18 Description: YcaO cyclodehydratase, ATP-ad Mg2+-binding Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (322 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1317.82 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF14028.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.tmp_proteins.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000021.43.PF14028.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Lant_dehydr_C [M=288] Accession: PF14028.8 Description: Lantibiotic biosynthesis dehydratase C-term Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (288 nodes) Target sequences: 6 (40926 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 285.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000491.44.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6772 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (187432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (187432 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2380.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (187432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 487.32 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (187432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6597.61 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (187432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 7890.89 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (187432 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2923.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (187432 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000111.45.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (187432 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (414758 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 7299.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (414758 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (414758 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8730.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (414758 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4354.96 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (414758 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5267.43 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (414758 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6470.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (414758 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6967.93 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000031.46.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (414758 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (55938 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (55938 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (55938 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 710.41 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (55938 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (55938 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (55938 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (55938 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000281.47.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (55938 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (10168 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (10168 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (10168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (10168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (10168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (10168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (10168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000441.48.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (10168 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (142818 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (142818 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5027.19 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (142818 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2399.34 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (142818 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (142818 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (142818 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (142818 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000141.4.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (142818 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (323984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 842.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (323984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3401.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (323984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1295.94 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (323984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 13639.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (323984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4114.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (323984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (323984 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5054.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000041.49.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (323984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5442.93 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (218586 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (218586 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3672.24 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (218586 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3409.94 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (218586 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (218586 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 9202.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (218586 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2295.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (218586 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7694.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000071.50.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (218586 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2776.04 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (60984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (60984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 951.35 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (60984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (60984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (60984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (60984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2567.43 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (60984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000271.51.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (60984 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (112616 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (112616 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 4741.13 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (112616 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1182.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (112616 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3964.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (112616 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1430.22 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (112616 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1756.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (112616 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000201.52.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (112616 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1891.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-08 21.9 0.1 2.2e-05 13.3 0.0 2.6 0 frame_6 Domain annotation for each sequence: >> frame_6 [No individual domains that satisfy reporting thresholds (although complete target did)] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (232244 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 1 (0.166667); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.09 # Mc/sec: 433.52 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (232244 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 1811.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (232244 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9777.47 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (232244 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 928.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (232244 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2949.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (232244 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (232244 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2438.56 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000061.53.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (232244 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8174.99 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (100084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (100084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1271.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (100084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 260.22 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (100084 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (100084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1050.88 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (100084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1681.41 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (100084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000221.54.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (100084 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4213.54 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 216.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 78.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 95.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000521.55.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6150 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 64.58 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (33904 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 355.99 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (33904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (33904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (33904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (33904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 135.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (33904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (33904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000311.56.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (33904 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 569.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (119766 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (119766 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (119766 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1521.03 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (119766 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5042.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (119766 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1257.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (119766 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (119766 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000161.57.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (119766 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (30364 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 385.62 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (30364 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 121.46 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (30364 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (30364 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (30364 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1068.81 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (30364 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1278.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (30364 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000351.58.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (30364 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 473.68 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (525268 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 2 (0.333333); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.09u 0.00s 00:00:00.09 Elapsed: 00:00:00.10 # Mc/sec: 882.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (525268 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 7371.26 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (525268 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 4097.09 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (525268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2101.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (525268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5515.31 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (525268 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 18489.43 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (525268 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1365.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125921.5.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (525268 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 3335.45 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (33402 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1406.22 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (33402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (33402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 561.15 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (33402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (33402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 350.72 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (33402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (33402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000321.59.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (33402 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 521.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (29828 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (29828 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 465.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (29828 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1049.95 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (29828 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (29828 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1255.76 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (29828 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (29828 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000361.60.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (29828 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (92722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (92722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (92722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3903.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (92722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (92722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (92722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1557.73 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (92722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 973.58 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000231.61.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (92722 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (30624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (30624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (30624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 79.62 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (30624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (30624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (30624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (30624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000331.62.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (30624 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (25434 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (25434 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (25434 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (25434 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (25434 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 101.74 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (25434 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (25434 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000371.63.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (25434 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 25.78 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 226.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6444 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6444 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000511.64.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6444 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (14636 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 616.18 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (14636 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (14636 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (14636 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (14636 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (14636 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (14636 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000391.65.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (14636 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (117210 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1828.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (117210 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (117210 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (117210 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1230.70 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (117210 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (117210 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (117210 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000171.66.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (117210 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (13850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 55.40 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (13850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 36.01 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (13850 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 487.52 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (13850 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (13850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 232.68 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (13850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 583.09 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (13850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000411.67.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (13850 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (66124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1031.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (66124 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 264.50 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (66124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 694.30 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (66124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2327.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (66124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (66124 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (66124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000261.68.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (66124 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (450702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9487.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (450702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1171.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (450702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5723.92 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (450702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (450702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7571.79 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (450702 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 3515.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (450702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 15864.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000061.6.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (450702 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (30396 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (30396 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (30396 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (30396 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (30396 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (30396 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (30396 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000341.69.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (30396 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (68176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 865.84 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (68176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (68176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (68176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (68176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1145.36 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (68176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (68176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000251.70.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (68176 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2399.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (22970 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 967.04 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (22970 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (22970 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 808.54 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (22970 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (22970 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (22970 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (22970 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000381.71.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (22970 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (8048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (8048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 84.50 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (8048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 283.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (8048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (8048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 32.19 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (8048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (8048 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 135.21 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000451.72.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (8048 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (6628 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 69.59 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (6628 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 233.31 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (6628 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (6628 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (6628 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (6628 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (6628 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000501.73.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (6628 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 84.18 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (85110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 221.29 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (85110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (85110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3583.13 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (85110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (85110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (85110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 893.65 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (85110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_ATMK010000241.74.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (85110 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (33844 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1424.83 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (33844 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 355.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (33844 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (33844 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (33844 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (33844 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (33844 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000421.75.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (33844 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (37736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 150.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (37736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (37736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1588.69 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (37736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (37736 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (37736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 479.25 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (37736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000581.76.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (37736 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (239708 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4027.09 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (239708 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (239708 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 958.83 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (239708 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10091.71 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (239708 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3739.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (239708 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 623.24 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (239708 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000691.77.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (239708 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (322200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3383.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (322200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 5412.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (322200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (322200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11341.44 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (322200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (322200 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 5026.32 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (322200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 13564.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000461.78.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (322200 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (74946 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3155.23 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (74946 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1169.16 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (74946 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (74946 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (74946 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (74946 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2638.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (74946 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 951.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KI9125911.7.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (74946 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (323724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11395.08 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (323724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 5438.56 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (323724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (323724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3399.10 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (323724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (323724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 13628.78 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (323724 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 5050.09 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832651.79.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (323724 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (25312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 65.81 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (25312 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (25312 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (25312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 890.98 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (25312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (25312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (25312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000391.80.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (25312 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (25474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (25474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (25474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 427.96 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (25474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (25474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 267.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (25474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (25474 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 397.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000401.81.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (25474 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (82568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1387.14 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (82568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (82568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (82568 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1288.06 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (82568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3476.11 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (82568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (82568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832641.82.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (82568 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (82582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (82582 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1288.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (82582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2906.89 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (82582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (82582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (82582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (82582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1387.38 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000141.83.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (82582 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (40810 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (40810 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1718.10 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (40810 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (40810 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1436.51 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (40810 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (40810 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (40810 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000531.84.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (40810 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (106360 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 1 (0.166667); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.03 # Mc/sec: 595.62 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (106360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1350.77 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (106360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3743.87 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (106360 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1659.22 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (106360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1116.78 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (106360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (106360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000591.85.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (106360 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 425.44 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (9264 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (9264 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (9264 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (9264 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (9264 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 326.09 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (9264 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (9264 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000471.86.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (9264 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (160498 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (160498 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (160498 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (160498 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (160498 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (160498 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2696.37 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (160498 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6756.97 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832671.87.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (160498 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2038.32 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (9884 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (9884 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (9884 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (9884 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (9884 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (9884 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (9884 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000081.88.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (9884 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 416.12 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (56416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 947.79 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (56416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (56416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 592.37 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (56416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 716.48 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (56416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (56416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 225.66 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (56416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_JAEZ010000241.8.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (56416 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (281646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 3576.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (281646 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4393.68 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (281646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 2957.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (281646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (281646 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11857.30 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (281646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4731.65 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (281646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000291.89.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (281646 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9913.94 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (10146 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (10146 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (10146 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (10146 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 106.53 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (10146 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (10146 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (10146 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 158.28 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000241.90.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (10146 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (71142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 2504.20 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (71142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (71142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (71142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (71142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (71142 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (71142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000271.91.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (71142 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1195.19 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (19190 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 675.49 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (19190 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 807.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (19190 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (19190 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (19190 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (19190 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (19190 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832661.92.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (19190 residues searched) Passed MSV filter: 3 (0.5); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 299.36 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (48974 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (48974 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (48974 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (48974 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 2061.81 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (48974 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (48974 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (48974 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000661.93.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (48974 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 822.76 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (19088 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (19088 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (19088 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (19088 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 320.68 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (19088 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 49.63 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (19088 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (19088 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 671.90 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000681.94.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (19088 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 803.60 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (72770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3063.62 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (72770 residues searched) Passed MSV filter: 2 (0.333333); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1135.21 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (72770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (72770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (72770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (72770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (72770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000451.95.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (72770 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (343356 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3605.24 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (343356 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 2884.19 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (343356 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7227.64 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (343356 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 2678.18 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (343356 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 4360.62 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (343356 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 1373.42 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (343356 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6043.07 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000281.96.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (343356 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 892.73 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (61466 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 1032.63 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (61466 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (61466 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (61466 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 645.39 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (61466 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (61466 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (61466 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_KQ9832601.97.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (61466 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF02794.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.PF02794.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: HlyC [M=127] Accession: PF02794.18 Description: RTX toxin acyltransferase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (127 nodes) Target sequences: 6 (79922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF05147.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.PF05147.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LANC_like [M=352] Accession: PF05147.15 Description: Lanthionine synthetase C-like protein Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (352 nodes) Target sequences: 6 (79922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/TIGR04195.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.TIGR04195.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04195 [M=421] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (421 nodes) Target sequences: 6 (79922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 3364.72 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF01944.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.PF01944.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoIIM [M=156] Accession: PF01944.19 Description: Stage II sporulation protein M Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 6 (79922 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/LinL.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.LinL.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LinL [M=26] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (26 nodes) Target sequences: 6 (79922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 207.80 // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/labKC.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.labKC.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: labKC [M=40] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (40 nodes) Target sequences: 6 (79922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok] # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/PF00881.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.PF00881.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Nitroreductase [M=168] Accession: PF00881.26 Description: Nitroreductase family Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (168 nodes) Target sequences: 6 (79922 residues searched) Passed MSV filter: 0 (0); expected 0.1 (0.02) Passed bias filter: 0 (0); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 1342.69 // [ok] Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h Incorrect number of command line arguments. Usage: hmmsearch [options] where most common options are: -h : show brief help on version and usage To see more help on available options, do /data/pg-molgen/software/bagel4/tools/hmmsearch/binaries/hmmsearch -h # hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: /data/pg-molgen/software/bagel4_2022/db_hmm/CyaG.hmm # target sequence database: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.six_frames.fna # per-dom hits tabular output: /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Prevotellaceae/PRevotella_intermedia.result/NZ_LBGT010000251.98.CyaG.domtblout # show alignments in output: no # domain reporting threshold: score >= 25 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CyaG [M=105] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each sequence: [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (105 nodes) Target sequences: 6 (79922 residues searched) Passed MSV filter: 1 (0.166667); expected 0.1 (0.02) Passed bias filter: 1 (0.166667); expected 0.1 (0.02) Passed Vit filter: 0 (0); expected 0.0 (0.001) Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 6 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: inf // [ok]