# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: pfam_list/TrmO.hmm.txt # target sequence database: proteomes/Monosiga_brevicollis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TrmO [M=119] Accession: PF01980.16 Description: tRNA-methyltransferase O Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-42 141.0 0.0 3e-41 139.4 0.0 1.9 2 tr|A9V4U4|A9V4U4_MONBE Predicted protein OS=Monosiga brevico 6.2e-08 31.9 0.0 1e-07 31.2 0.0 1.5 1 tr|A9V8A2|A9V8A2_MONBE Predicted protein OS=Monosiga brevico Domain annotation for each sequence (and alignments): >> tr|A9V4U4|A9V4U4_MONBE Predicted protein OS=Monosiga brevicollis OX=81824 GN=33342 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.3 0.0 1.2 5.4e+03 31 86 .. 541 596 .. 529 603 .. 0.56 2 ! 139.4 0.0 6.5e-45 3e-41 1 119 [] 967 1084 .. 967 1084 .. 0.98 Alignments for each domain: == domain 1 score: -3.3 bits; conditional E-value: 1.2 GGG-SEEEEEEE-TTS......-.SS--E-TT-.SS-E.EGGGS--S-SSS-EEEEEEE CS TrmO 31 leefshlwllfvfhen...aekklkakvrpprlggnervGvfatRsphRpnpiglsvvk 86 l +f+ lw vf+++ +++++ a+ +p +++ +at i +svv+ tr|A9V4U4|A9V4U4_MONBE 541 LANFDALWADSVFDSRedlQAATTGATSLKPLTNE---APAMATNRADSAQVIIVSVVR 596 78889999999998662332222233333444333...244666666666666666665 PP == domain 2 score: 139.4 bits; conditional E-value: 6.5e-45 TS-SSGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SSS-EEEEEE CS TrmO 1 giPrqpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRpnpiglsvv 85 g+Prqp+l++ ++a+++l+ +++ alegl+++sh+w++f fh n++ ++k+k+rpp+ gg rvGv+atRsphRpnpigls++ tr|A9V4U4|A9V4U4_MONBE 967 GTPRQPNLCPMSRAKLRLRCFNDNHPALEGLHHYSHVWIIFLFHLNDNVAVKPKIRPPKAGG-LRVGVMATRSPHRPNPIGLSLC 1050 79*****************9999*********************9989999*********99.999******************* PP EEEEEETTEEEEES----TT-EEEEEEE--HHHH CS TrmO 86 klekvegnvlevsgvDlldgtpvlDiKPYvpyaD 119 k++++eg+++ ++g+Dl+dgtpvlD+KPY+p++D tr|A9V4U4|A9V4U4_MONBE 1051 KVHRIEGDTIILAGIDLVDGTPVLDVKPYLPFFD 1084 *******************************999 PP >> tr|A9V8A2|A9V8A2_MONBE Predicted protein OS=Monosiga brevicollis OX=81824 GN=11127 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 31.2 0.0 2.2e-11 1e-07 92 118 .. 37 63 .. 6 64 .. 0.85 Alignments for each domain: == domain 1 score: 31.2 bits; conditional E-value: 2.2e-11 TTEEEEES----TT-EEEEEEE--HHH CS TrmO 92 gnvlevsgvDlldgtpvlDiKPYvpya 118 + ++g Dl+dgtpvlDiKPY+p++ tr|A9V8A2|A9V8A2_MONBE 37 AAGIAIAGHDLVDGTPVLDIKPYLPHV 63 46699*******************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (119 nodes) Target sequences: 9188 (5511963 residues searched) Passed MSV filter: 135 (0.0146931); expected 183.8 (0.02) Passed bias filter: 129 (0.0140401); expected 183.8 (0.02) Passed Vit filter: 13 (0.00141489); expected 9.2 (0.001) Passed Fwd filter: 2 (0.000217675); expected 0.1 (1e-05) Initial search space (Z): 9188 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 16398.09 // [ok]