# hmmscan :: search sequence(s) against a profile database # HMMER 3.0 (March 2010); http://hmmer.org/ # Copyright (C) 2010 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: s01.fasta # target HMM database: /home/bow/db/hmmer/Pfam-A.hmm # output directed to file: hmmer_cases/text_hmmscan_s01.out # per-seq hits tabular output: hmmer_cases/tab_hmmscan_s01.out # per-dom hits tabular output: hmmer_cases/domtab_hmmscan_s01.out # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|4885477|ref|NP_005359.1| [L=154] Description: myoglobin [Homo sapiens] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-21 74.6 0.3 9.2e-21 74.0 0.2 1.3 1 Globin Globin Domain annotation for each model (and alignments): >> Globin Globin # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 74.0 0.2 6.7e-25 9.2e-21 1 107 [. 7 112 .. 7 113 .. 0.97 Alignments for each domain: == domain 1 score: 74.0 bits; conditional E-value: 6.7e-25 HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHSGGGGGGGCCCTTTT.HHHHHTSCHHHHHHHHHHHHHHHHHHCTTSHHHHHH CS Globin 1 qkalvkaswekvkanaeeigaeilkrlfkaypdtkklFkkfgdls.aedlksspkfkahakkvlaaldeavknldnddnlka 81 +++lv w+kv+a+++ +g+e+l rlfk +p+t ++F kf+ l+ +++k s+++k+h+++vl al+ ++k+ ++ ++a gi|4885477|ref|NP_005359.1| 7 EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKsEDEMKASEDLKKHGATVLTALGGILKK---KGHHEA 85 5789*********************************************************************...6899** PP HHHHHHHHHHTT-.--HHHHCCHHHHH CS Globin 82 alkklgarHakrg.vdpanfklfgeal 107 ++k l+++Ha+++ ++ ++ + ++e++ gi|4885477|ref|NP_005359.1| 86 EIKPLAQSHATKHkIPVKYLEFISECI 112 *********************999998 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (154 residues) Target model(s): 13672 (2396357 nodes) Passed MSV filter: 458 (0.0334991); expected 273.4 (0.02) Passed bias filter: 404 (0.0295494); expected 273.4 (0.02) Passed Vit filter: 31 (0.00226741); expected 13.7 (0.001) Passed Fwd filter: 1 (7.31422e-05); expected 0.1 (1e-05) Initial search space (Z): 13672 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.28u 0.17s 00:00:00.45 Elapsed: 00:00:00.21 # Mc/sec: 1757.33 //