# 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/Trypanosoma_brucei.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-47 159.7 0.0 5.1e-44 149.9 0.0 3.2 2 tr|Q57XW9|Q57XW9_TRYB2 Cytosine-specific DNA methylase, puta ------ inclusion threshold ------ 0.04 12.2 0.0 0.067 11.5 0.0 1.3 1 tr|Q38BT8|Q38BT8_TRYB2 Uncharacterized protein OS=Trypanosom Domain annotation for each sequence (and alignments): >> tr|Q57XW9|Q57XW9_TRYB2 Cytosine-specific DNA methylase, putative OS=Trypanosoma brucei brucei (strain 927/4 GUTat10. # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 149.9 0.0 1.2e-47 5.1e-44 1 308 [. 226 562 .. 226 576 .. 0.77 2 ! 5.8 0.0 0.00084 3.6 312 333 .. 594 615 .. 585 617 .. 0.88 Alignments for each domain: == domain 1 score: 149.9 bits; conditional E-value: 1.2e-47 -EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-...................-SEEEES-TTTS-GS--.-SEEEE-- CS DNA_methylase 1 lkfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk..................kvsigDitkidkkklpediDlLvgGf 69 ++f +LfaG+G fr+gle++g++cv+a+e ++a +Y+an++ + gDit++ +p+ +D+L++Gf tr|Q57XW9|Q57XW9_TRYB2 226 FTFSELFAGMGMFRVGLERIGGKCVFAVECAPHARSVYHANHHlprrnscgnealpatrrpVPLVGDITTVPSHYFPH-HDVLTAGF 311 6899****************************************998777777777666544456788888888***5.******** PP -GGGTECTSEE--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCS............HHHHHHHHHHHH........HTEE CS DNA_methylase 70 PCqpfSvaGkqkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkg............ktlkvileklee........lGYe 136 PCq+f +aG+ +g dt+g+Lf+e++r+i++ kPk fllENV+++l+ + + lk il++l++ l Y tr|Q57XW9|Q57XW9_TRYB2 312 PCQSFAKAGSATGLRDTKGQLFYEVVRVIQSAKPKGFLLENVENVLHVGGEdggeanaseesqHHLKFILDALRSpspdsneaLTYV 398 *********************************************98755566788899999999******99753333322256** PP EEEEEEEGGGTT-SB--EEEEEEEEEGGG---........-------SS---GGG.....TSGGGTTS-EEBTTTB--GGGSSSTT- CS DNA_methylase 137 vsykllnasdyGvpQnReRvfivgirkdleln........vlvkvkefrfpkkkdleasktlrdlleekseldeektalsdklveke 215 v y++++ + +pQ+R+R ++vgir dl+ + +v + r + + + ea +rd+l++ ++e+ +++++lv+ tr|Q57XW9|Q57XW9_TRYB2 399 VAYRVIDGALV-TPQRRRRAYFVGIRADLPRAnardvgavLDDAVRQLRAYRDMHPEAPRCVRDILDST-GDTSEMGEFNQSLVSLR 483 *******9976.9****************8767887776644555555555554477888999999973.45666666666666555 PP EE--.......S---HHHTS--..B--TTS...-B----S-STT--B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT- CS DNA_methylase 216 ekikkttkaseegypkelsrnr..idkveelkglsatrrksgrgeklekelaeagklqknkerfkpviekkriRrLtprEaarlqGf 300 + +++ +++ +++ +r v +l+gl +t + s r + +l+ + ++ + R + rE+arlqG tr|Q57XW9|Q57XW9_TRYB2 484 LTE-----SQWAAVQRSVTFRRspSWRVSDLNGLARTLMGSYR---ASYQLYSEFVPLPDGG--------PPFRFYSIRECARLQGI 554 544.....45666665333443225556666666666666665...3334444444444444........578999*********** PP -TT----- CS DNA_methylase 301 Pddfefgs 308 Pd+f f + tr|Q57XW9|Q57XW9_TRYB2 555 PDWFSFNV 562 ****9975 PP == domain 2 score: 5.8 bits; conditional E-value: 0.00084 HHHHHHHTS--HHHHHHHHHHH CS DNA_methylase 312 aaykqiGnsVpvpvieaiakei 333 a+yk+iGn+V++ v+e +++++ tr|Q57XW9|Q57XW9_TRYB2 594 AVYKLIGNAVNPIVVECLGRAL 615 78**************999987 PP >> tr|Q38BT8|Q38BT8_TRYB2 Uncharacterized protein OS=Trypanosoma brucei brucei (strain 927/4 GUTat10.1) OX=185431 GN=Tb # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.5 0.0 1.6e-05 0.067 3 43 .. 231 272 .. 230 304 .. 0.85 Alignments for each domain: == domain 1 score: 11.5 bits; conditional E-value: 1.6e-05 EEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-. CS DNA_methylase 3 fidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk 43 ++d+faGiG f+l l+ g +++v a e++k+ a ++ n tr|Q38BT8|Q38BT8_TRYB2 231 VVDMFAGIGYFTLPLAINGgVKIVHALEKNKYSALYLAFNAV 272 69**************998899********998777666664 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (335 nodes) Target sequences: 8561 (4332363 residues searched) Passed MSV filter: 484 (0.0565355); expected 171.2 (0.02) Passed bias filter: 223 (0.0260484); expected 171.2 (0.02) Passed Vit filter: 17 (0.00198575); expected 8.6 (0.001) Passed Fwd filter: 3 (0.000350426); expected 0.1 (1e-05) Initial search space (Z): 8561 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.15u 0.01s 00:00:00.16 Elapsed: 00:00:00.08 # Mc/sec: 18141.77 // [ok]