# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (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/DNA_methylase.hmm.txt # target sequence database: proteomes/Trichomonas_vaginalis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: DNA_methylase [M=335] Accession: PF00145.17 Description: C-5 cytosine-specific DNA methylase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- ------ inclusion threshold ------ 0.12 13.1 3.7 0.14 12.9 3.7 1.1 1 tr|A2DXF4|A2DXF4_TRIVA Uncharacterized protein OS=Trichomona 0.6 10.9 15.1 0.73 10.6 15.1 1.0 1 tr|A2GTU6|A2GTU6_TRIVA Neurofilament triplet M protein, puta Domain annotation for each sequence (and alignments): >> tr|A2DXF4|A2DXF4_TRIVA Uncharacterized protein OS=Trichomonas vaginalis OX=5722 GN=TVAG_380160 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.9 3.7 5.8e-06 0.14 173 302 .. 42 165 .. 19 178 .. 0.61 Alignments for each domain: == domain 1 score: 12.9 bits; conditional E-value: 5.8e-06 ---SS---GGG.....TSGGGTTS-EEBTTTB--GGGSSSTT-EE--........S---HHHTS--.B--TTS...-B----S-ST. CS DNA_methylase 173 vkefrfpkkkdleasktlrdlleekseldeektalsdklvekeekikkttkase.egypkelsrnr.idkveelkglsatrrksgr. 256 +++ + p++ + ++++d++e+++ +e+++l ++++ek+ +++++++++e e y+ +l +r ++++++ ++s t + ++ tr|A2DXF4|A2DXF4_TRIVA 42 LQDGTNPDQ--QTCLSIINDVKEKRIAQADERYKLRTEIIEKQTEKEREKIKQEqEEYK-KLLFERlVRSYYQ-AYQSVTAQLKDLm 124 334444444..47899**********9***************99998888766516677.5555552444444.4444444444430 PP T--B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--T CS DNA_methylase 257 geklekelaeagklqknkerfkpviekkriRrLtprEaarlqGfPd 302 g+ ++++ ++g++ n + r+ p+E a++ P tr|A2DXF4|A2DXF4_TRIVA 125 GKDYSQYISQNGITFPNIPSE-----VQMRTRMQPNEEAKIKLTPA 165 333344444444444444421.....12222455555555544444 PP >> tr|A2GTU6|A2GTU6_TRIVA Neurofilament triplet M protein, putative (Fragment) OS=Trichomonas vaginalis OX=5722 GN=TVAG # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.6 15.1 2.9e-05 0.73 173 314 .. 14 154 .. 2 163 .. 0.51 Alignments for each domain: == domain 1 score: 10.6 bits; conditional E-value: 2.9e-05 ---SS---GGG.....TSGGGTTS-EEBTTTB--GGGSSSTT-EE--.......S---HHHTS--...B--TTS...-B----S-ST CS DNA_methylase 173 vkefrfpkkkdleasktlrdlleekseldeektalsdklvekeekikkttkaseegypkelsrnr...idkveelkglsatrrksgr 256 e+++pkkk+ ++++ ++++e++ + + + a +++ +++ k k++kas+e+ e+ ++ + +++++ ++ t+rk ++ tr|A2GTU6|A2GTU6_TRIVA 14 DLEEEKPKKKK--SKQIENEIEEKP--KRKGRKAQNNEPDDEKPKE-KRSKASKENQV-EEKPKKkgkKHDTNDSDKEINTKRKGKK 94 23334444432..444444444443..2222222222222222222.22333322222.1111112224555555556666666554 PP T--B-TTS---EEEETTEEE--T....TTGGG--B-BHHHHHHHHT--TT-----SBH.HHH CS DNA_methylase 257 geklekelaeagklqknkerfkp...viekkriRrLtprEaarlqGfPddfefgskks.aay 314 ++e+ ++ kl+k+k++ + ie++++ + + r+ G P +fef + + +++ tr|A2GTU6|A2GTU6_TRIVA 95 --VVEEIPEKTKKLRKTKSQEETsstDIEHQKEQSFVIDAGNRIEGTPVNFEFNPHPKvEQT 154 ..44444444555555555444477899*************************987665555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (335 nodes) Target sequences: 50190 (17055200 residues searched) Passed MSV filter: 6805 (0.135585); expected 1003.8 (0.02) Passed bias filter: 1338 (0.0266587); expected 1003.8 (0.02) Passed Vit filter: 218 (0.00434349); expected 50.2 (0.001) Passed Fwd filter: 29 (0.000577804); expected 0.5 (1e-05) Initial search space (Z): 50190 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 1.83u 0.06s 00:00:01.89 Elapsed: 00:00:00.59 # Mc/sec: 9683.88 // [ok]