# nhmmer :: search a DNA model or alignment against a DNA database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query file: /usr/local/src/CheckM-1.0.7/data/hmms_ssu/SSU_bacteria.hmm # target sequence database: - # output directed to file: ssu/ssu.bacteria.txt # hits tabular output: ssu/ssu.bacteria.table.txt # show alignments in output: no # sequence reporting threshold: E-value <= 1e-05 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: bacteria [M=1523] Scores for complete hits: E-value score bias Sequence start end Description ------- ------ ----- -------- ----- ----- ----------- 0 1332.9 42.8 CARPRO_18 5172 3641 id=20114 bin=CARPRO alias=CARPRO_23 0 1324.6 13.9 CARSEP3_4 1460 5 id=20220 bin=CARSEP3 alias=CARSEP3_560 1e-263 879.4 15.9 CARSEP3_12 1006 1 id=20228 bin=CARSEP3 alias=CARSEP3_523 3.1e-209 698.9 14.4 CARSEP3_8 66306 67140 id=20224 bin=CARSEP3 alias=CARSEP3_507 1e-185 621.0 14.9 CAREFA_8 789 2 id=20265 bin=CAREFA alias=CAREFA_6 4.1e-184 615.7 12.7 CARSEP3_17 768 1 id=20233 bin=CARSEP3 alias=CARSEP3_528 1.3e-176 590.8 13.3 CARSEP3_14 84778 85517 id=20230 bin=CARSEP3 alias=CARSEP3_505 1.8e-175 587.1 14.5 CAREFA_7 63090 63843 id=20264 bin=CAREFA 5.6e-174 582.2 14.6 CAREFA_6 752 1 id=20263 bin=CAREFA alias=CAREFA_5 2.8e-14 53.2 0.5 CARSEP_3 102 31 id=20123 bin=CARSEP alias=CARSEP_606 2.9e-14 53.2 0.7 CARSEP_14 63916 63987 id=20134 bin=CARSEP alias=CARSEP_661 3.1e-14 53.1 0.7 CARSEP_10 84421 84493 id=20130 bin=CARSEP alias=CARSEP_655 3.1e-14 53.1 0.7 CARSEP_12 103 31 id=20132 bin=CARSEP alias=CARSEP_653 3.1e-14 53.1 0.7 CARSEP_2 103 31 id=20122 bin=CARSEP alias=CARSEP_646 Annotation for each hit : >> CARPRO_18 id=20114 bin=CARPRO alias=CARPRO_23 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 1332.9 42.8 0 28 1514 .. 5172 3641 .. 5193 3631 .. 5368 0.95 >> CARSEP3_4 id=20220 bin=CARSEP3 alias=CARSEP3_560 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 1324.6 13.9 0 29 1411 .. 1460 5 .. 1481 1 .. 185661 0.94 >> CARSEP3_12 id=20228 bin=CARSEP3 alias=CARSEP3_523 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 879.4 15.9 1e-263 29 964 .. 1006 1 .. 1027 1 .. 128367 0.93 >> CARSEP3_8 id=20224 bin=CARSEP3 alias=CARSEP3_507 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 698.9 14.4 3.1e-209 29 797 .. 66306 67140 .. 66285 67141 .] 67141 0.92 >> CAREFA_8 id=20265 bin=CAREFA alias=CAREFA_6 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 621.0 14.9 1e-185 25 735 .. 789 2 .. 809 1 .. 222047 0.91 >> CARSEP3_17 id=20233 bin=CARSEP3 alias=CARSEP3_528 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 615.7 12.7 4.1e-184 29 730 .. 768 1 .. 789 1 .. 40854 0.91 >> CARSEP3_14 id=20230 bin=CARSEP3 alias=CARSEP3_505 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 590.8 13.3 1.3e-176 29 703 .. 84778 85517 .] 84757 85517 .] 85517 0.91 >> CAREFA_7 id=20264 bin=CAREFA score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 587.1 14.5 1.8e-175 25 702 .. 63090 63843 .] 63070 63843 .] 63843 0.91 >> CAREFA_6 id=20263 bin=CAREFA alias=CAREFA_5 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 582.2 14.6 5.6e-174 26 701 .. 752 1 .. 773 1 .. 280602 0.91 >> CARSEP_3 id=20123 bin=CARSEP alias=CARSEP_606 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 53.2 0.5 2.8e-14 31 102 .. 102 31 .. 121 10 .. 71143 0.83 >> CARSEP_14 id=20134 bin=CARSEP alias=CARSEP_661 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 53.2 0.7 2.9e-14 31 102 .. 63916 63987 .. 63897 64008 .. 64017 0.83 >> CARSEP_10 id=20130 bin=CARSEP alias=CARSEP_655 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 53.1 0.7 3.1e-14 30 102 .. 84421 84493 .. 84402 84514 .. 84523 0.83 >> CARSEP_12 id=20132 bin=CARSEP alias=CARSEP_653 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 53.1 0.7 3.1e-14 30 102 .. 103 31 .. 122 10 .. 83310 0.83 >> CARSEP_2 id=20122 bin=CARSEP alias=CARSEP_646 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 53.1 0.7 3.1e-14 30 102 .. 103 31 .. 122 10 .. 40512 0.83 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1523 nodes) Target sequences: 2320 (56837224 residues searched) Residues passing SSV filter: 633639 (0.0111); expected (0.02) Residues passing bias filter: 625072 (0.011); expected (0.02) Residues passing Vit filter: 58372 (0.00103); expected (0.003) Residues passing Fwd filter: 13015 (0.000229); expected (3e-05) Total number of hits: 14 (0.000158) # CPU time: 9.00u 0.19s 00:00:09.19 Elapsed: 00:00:01.19 # Mc/sec: 72742.09 // [ok]