# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (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/Monosiga_brevicollis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-29 99.9 0.0 1.2e-27 96.2 0.0 2.1 1 tr|A9UPS1|A9UPS1_MONBE Uncharacterized protein (Fragment) OS ------ inclusion threshold ------ 0.034 12.5 0.0 0.057 11.8 0.0 1.3 1 tr|A9V7D5|A9V7D5_MONBE Predicted protein OS=Monosiga brevico 0.069 11.5 0.1 0.13 10.7 0.0 1.4 2 tr|A9UP83|A9UP83_MONBE Uncharacterized protein OS=Monosiga b Domain annotation for each sequence (and alignments): >> tr|A9UPS1|A9UPS1_MONBE Uncharacterized protein (Fragment) OS=Monosiga brevicollis OX=81824 GN=1464 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 96.2 0.0 4e-31 1.2e-27 37 330 .. 1 354 [. 1 355 [. 0.66 Alignments for each domain: == domain 1 score: 96.2 bits; conditional E-value: 4e-31 HHHHH-...-SEEEES-TTTS-GS--..-SEEEE---GGGTECTSEE--TTSGGGHHHHHHHHHHHHH-..-SEEEEEEEGGGGGGC CS DNA_methylase 37 tYeanfk..kvsigDitkidkkklpe.diDlLvgGfPCqpfSvaGkqkgfedtrgtLffeiiriikekk..PkvfllENVkgLlkhd 118 +Y+an++ ++ +i+ + +++l++ Dl + ++PCqp+S +G+q+g ed r++ f + + + k P v+l ENV g +++ tr|A9UPS1|A9UPS1_MONBE 1 VYQANHPdtLIKNRNIQAVPIRQLEKlAADLWLMSPPCQPYSRQGHQRGLEDARSDSFRYLLDALTQMKnpPSVILVENVVGFESSQ 87 7*****9765667788888888999888************************************9998888***********99996 PP CSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB--EEEEEEEEEGGG---........-------SS---GGG.............. CS DNA_methylase 119 kgktlkvilekleelGYevsykllnasdyGvpQnReRvfivgirkdleln........vlvkvkefrfpkkkd.............. 183 ++++ +l+ l Y+++ l ++Gvp +R R f+++ir d+ f + + tr|A9UPS1|A9UPS1_MONBE 88 G---REELVATLNTLQYRFQEFWLSPDQFGVPNSRLRYFLLAIRGDRFRAepsataadA-------AFGNSSTlmyhlpgalqfepg 164 6...556788899999*****************************97443533333330.......333333233333333333333 PP .......TSGGGTTS-EEBTTTB--GGGSSSTT-EE--.......S---H.....HHTS--.......................... CS DNA_methylase 184 ..leasktlrdlleekseldeektalsdklvekeekikkttkaseegypk.....elsrnr.......................... 237 +++ +t+ + ++ ++++ s +yp+ e tr|A9UPS1|A9UPS1_MONBE 165 lpTSEFGTF---------------------DDAYRVAVEQSQVSDYSYPQqvciaE----Acaigskkkknnagcltshpprmgils 226 331111122.....................22222222222222222222211110....111111111222333333333344444 PP .............................B--TTS...-B----S-STT--B-TTS---EEEETTEEE--T............TTGG CS DNA_methylase 238 .............................idkveelkglsatrrksgrgeklekelaeagklqknkerfkp...........viekk 284 ++ +kg+s++++ +g+ + + ++ ++ + f++ +e tr|A9UPS1|A9UPS1_MONBE 227 sthlarhlpgsgrlllrwgrlldivrpeeRRSLCFTKGYSHKVEGTGS-------VFQVCICVAIPMAFEQldvpspgagwpAVEAL 306 444555666666676666777776666655566666666666666664.......33333333333333335566677788889999 PP G--B-BHHHHHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHH CS DNA_methylase 285 riRrLtprEaarlqGfPddfefgskks..aaykqiGnsVpvpvieaia 330 + R +tp+E+ rl GfP df ++s+ + +a+k iGns+ v+++ +++ tr|A9UPS1|A9UPS1_MONBE 307 ELRYFTPQEMLRLHGFPTDFVIPSSVTdrQARKAIGNSLCVTIVAHLL 354 *************************9999*************999875 PP >> tr|A9V7D5|A9V7D5_MONBE Predicted protein OS=Monosiga brevicollis OX=81824 GN=28161 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.8 0.0 1.9e-05 0.057 3 44 .. 240 290 .. 239 305 .. 0.78 Alignments for each domain: == domain 1 score: 11.8 bits; conditional E-value: 1.9e-05 EEEES-TT-HHHHH.HHHTT-EEEEEEE--TTTHHHHHHH-.........- CS DNA_methylase 3 fidLfaGiGGfrlg.leaagfecvaaseidkkaaktYeanfk........k 44 ++dLfaGiG f+l l a + a e++++a++ +++n k + tr|A9V7D5|A9V7D5_MONBE 240 VVDLFAGIGYFTLPyLVHARARFLHACEWNPHAVEALRRNLKlnqvadrcE 290 79***********8456777********************98765333333 PP >> tr|A9UP83|A9UP83_MONBE Uncharacterized protein OS=Monosiga brevicollis OX=81824 GN=14119 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.7 0.0 4.1e-05 0.13 2 37 .. 52 87 .. 51 104 .. 0.88 2 ? -3.5 0.0 0.81 2.5e+03 300 311 .. 187 198 .. 170 202 .. 0.72 Alignments for each domain: == domain 1 score: 10.7 bits; conditional E-value: 4.1e-05 EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHH CS DNA_methylase 2 kfidLfaGiGGfrlgleaagfecvaaseidkkaakt 37 +++dL +G+G ++++ + g ++v+a++id a ++ tr|A9UP83|A9UP83_MONBE 52 TVVDLGCGCGMLSIACALQGADHVLAVDIDSAALDI 87 589****************************99876 PP == domain 2 score: -3.5 bits; conditional E-value: 0.81 --TT-----SBH CS DNA_methylase 300 fPddfefgskks 311 +P++++f+ k+s tr|A9UP83|A9UP83_MONBE 187 LPKTYKFHNKQS 198 577777777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (335 nodes) Target sequences: 9188 (5511963 residues searched) Passed MSV filter: 555 (0.0604049); expected 183.8 (0.02) Passed bias filter: 301 (0.0327601); expected 183.8 (0.02) Passed Vit filter: 40 (0.0043535); expected 9.2 (0.001) Passed Fwd filter: 4 (0.00043535); expected 0.1 (1e-05) Initial search space (Z): 9188 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.18u 0.01s 00:00:00.19 Elapsed: 00:00:00.06 # Mc/sec: 30775.13 // [ok]