# 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/Ciona_savignyi.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-48 162.7 0.0 1.9e-47 161.6 0.0 1.6 1 tr|H2YXW1|H2YXW1_CIOSA Cytosine-specific methyltransferase O 3.3e-40 137.8 0.0 4.8e-40 137.3 0.0 1.2 1 tr|H2Y5J5|H2Y5J5_CIOSA Uncharacterized protein OS=Ciona savi 2e-18 66.2 0.0 9.9e-18 63.9 0.0 1.9 2 tr|H2YJ39|H2YJ39_CIOSA Uncharacterized protein OS=Ciona savi 1.2e-17 63.6 0.0 2e-14 53.1 0.0 2.2 2 tr|H2ZR26|H2ZR26_CIOSA Uncharacterized protein OS=Ciona savi 0.0015 17.3 0.0 0.0021 16.9 0.0 1.2 1 tr|H2Y5Z0|H2Y5Z0_CIOSA Uncharacterized protein OS=Ciona savi ------ inclusion threshold ------ 0.047 12.4 0.1 0.072 11.8 0.1 1.3 1 tr|H2ZQD2|H2ZQD2_CIOSA Uncharacterized protein OS=Ciona savi Domain annotation for each sequence (and alignments): >> tr|H2YXW1|H2YXW1_CIOSA Cytosine-specific methyltransferase OS=Ciona savignyi OX=51511 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 161.6 0.0 1e-50 1.9e-47 3 333 .. 808 1260 .. 806 1261 .] 0.78 Alignments for each domain: == domain 1 score: 161.6 bits; conditional E-value: 1e-50 EEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-............GS--...-SEEEE--- CS DNA_methylase 3 fidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk..kvsigDitkidkk............klpe..diDlLvgGfP 70 ++d f+G+GG++ g+++ag e +a+e ++ aa+ Y+ n++ +v ++D + + + lp+ d++lL+gG+P tr|H2YXW1|H2YXW1_CIOSA 808 TLDVFSGCGGLSEGFHQAGiAEPAYAIELWEPAAQAYRLNNPgaSVFTEDCNVLLEMvmngkersecgqRLPQkgDVELLCGGPP 892 78*****************99**********************977777777665556666777999999998667********* PP GGGTECTSE..E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB-- CS DNA_methylase 71 CqpfSvaGk..qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnasdyGvpQnR 153 Cq+fS ++ + +++L + + + + ++P +fllENV++ ++ ++ +lk l +l +GY++++ +l+a +yGv+Q R tr|H2YXW1|H2YXW1_CIOSA 893 CQGFSGMNRfnSREYSRFKNSLVVSYLSYCDYYRPRFFLLENVRNFVSFKNCMVLKLSLAALLRMGYQCTFGILQAGNYGVSQTR 977 *****998833445555556***************************************************************** PP EEEEEEEEEGGG----------SS---GGG.....TSGGGTTS-EE.....BTTTB--GGGSSSTT-EE--.......S---H.. CS DNA_methylase 154 eRvfivgirkdlelnvlvkvkefrfpkkkdleasktlrdlleekse.....ldeektalsdklvekeekikkttkaseegypk.. 231 +R +i++ +++l + ++++ +f++ + s ++ d++ + + + +t ++ +++ ki + +++ e +y+ tr|H2YXW1|H2YXW1_CIOSA 978 RRAIILAAAPGEKL-PFYPEPLHTFSTRGG-SLSAQVGDVKYTN-NikwtpSAPLRTITVRDAMSDLPKIPNGHSKAEMAYRGes 1059 **********9977.577777778887775.6667777766553.2346666667777777778888888777777777777433 PP HHTS--...............................................................B--TTS...-B----S CS DNA_methylase 232 elsrnr...............................................................idkveelkglsatrrk 253 + + + +++ tr|H2YXW1|H2YXW1_CIOSA 1060 Q---SHfqrmirgrdfqgvlrdhickdmsalvaarmelipllpgsdwrgptegtnrislsdgsmtkvlrY-----------DYHD 1130 2...33344666677777777888888899999999*******999999999999988665555544441...........3333 PP -STT-......................................................-B-TTS---EEEETTEEE--T.TTGG CS DNA_methylase 254 sgrge......................................................klekelaeagklqknkerfkpviekk 284 +++g+ ++ +++ ++++k+++ v++++ tr|H2YXW1|H2YXW1_CIOSA 1131 KKQGKsstganrgvcscaegkqcdpmdrqfntlvpwclphtgnrhnnwaglygrlgwdgYFSTTVTNPEPMGKQGR----VLHPE 1211 3333344444544555666667777777666666666666666666666666666555566666666666666666....9**** PP G--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHH CS DNA_methylase 285 riRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakei 333 ++R ++rE+ar qGfPd++ f ++ ++ + +Gn+Vp+p+ +ai+ ei tr|H2YXW1|H2YXW1_CIOSA 1212 QHRVVSVRECARSQGFPDSYRFFGTIMDKHREVGNAVPPPMSKAIGLEI 1260 *********************************************9886 PP >> tr|H2Y5J5|H2Y5J5_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 137.3 0.0 2.5e-43 4.8e-40 1 330 [. 5 372 .. 5 375 .] 0.75 Alignments for each domain: == domain 1 score: 137.3 bits; conditional E-value: 2.5e-43 -EEEEES-TT-HHHHHHHHTT...-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-GS--..-SEEEE---GGGTECTSEE- CS DNA_methylase 1 lkfidLfaGiGGfrlgleaag...fecvaaseidkkaaktYeanfk..kvsigDitkidkkklpe.diDlLvgGfPCqpfSvaGkqk 81 lk+++L +GiGG++++l g e+v++++i + a +Y+ nf+ + + i+ ++ +++ + ++ ++PCqpf G qk tr|H2Y5J5|H2Y5J5_CIOSA 5 LKVLELYSGIGGMHYALLDGGyanAEVVCSIDISPAASLVYKHNFPctTHCERSIEGFSAEDFDRmGFNTIMMSPPCQPFTRLGLQK 91 589**************99998889**********************999999***********977******************** PP -TTSGGGHHHHHHHHHHHHH-..-SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB--EEEEEEEEEGGG- CS DNA_methylase 82 gfedtrgtLffeiiriikekk..PkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnasdyGvpQnReRvfivgirkdle 166 + +d+r+ f ++++ + + P+++l+ENVkg ++ k+ + +++ l++lG++v ll +++G+p +R R ++++ ++++e tr|H2Y5J5|H2Y5J5_CIOSA 92 DVDDPRSRSFLHLMKLLPAMQspPNYILMENVKGFENS---KAHELFCKVLKQLGFSVVEFLLSPKQFGIPNSRLRYYLLAKHNQKE 175 ******************99999***********9888...668889999**********************************998 PP --.............................-------SS---GGG.....TSGGGTTS-EE....BTTTB--GGGSSSTT-EE--. CS DNA_methylase 167 ln.............................vlvkvkefrfpkkkdleasktlrdlleekse....ldeektalsdklvekeekikk 220 v+++++ r+ k+ +++k l++++ + + ++ ++ +++ +++ e++ + tr|H2Y5J5|H2Y5J5_CIOSA 176 FPdevnqlgkvfddiplclkrffliypiesiVPNQTQLGRKWKE---DQTKHLASYFVLLVLvgiiYRSKFESSKENPTKTLEQFLE 259 77888888888888888888887777644442222222222222...2344444444432224444444444444444444444444 PP ......S---HHHTS--.................B--TTS...-B----S-STT--B-TTS---EEEETTEEE--T.TTGGG--B-B CS DNA_methylase 221 ttkaseegypkelsrnr.................idkveelkglsatrrksgrgeklekelaeagklqknkerfkpviekkriRrLt 290 + ++ ++ y + k+ + ++s +++ g ++ ++g++ + ++ + ++ R +t tr|H2Y5J5|H2Y5J5_CIOSA 260 EPSSISDEYG------LpektllrylnvmdivnpVSKSSTCFTKSYGYYAEGT-----GSVLNTGSTLDMSN-----VLANKLRYFT 330 4444444443......0222222223344444445555555555555555553.....55666666666666.....67899***** PP HHHHHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHH CS DNA_methylase 291 prEaarlqGfPddfefgskks..aaykqiGnsVpvpvieaia 330 p E+a l++fP++f f+ + ++yk++Gns++v v+ ++ tr|H2Y5J5|H2Y5J5_CIOSA 331 PTEVANLMCFPEQFSFPDGFTrkQKYKLLGNSLNVYVVSCLL 372 ****************9866666**************98766 PP >> tr|H2YJ39|H2YJ39_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 63.9 0.0 5.1e-21 9.9e-18 1 115 [. 11 145 .. 11 158 .. 0.86 2 ? -0.1 0.0 0.16 3.1e+02 259 305 .. 213 259 .. 183 267 .. 0.81 Alignments for each domain: == domain 1 score: 63.9 bits; conditional E-value: 5.1e-21 -EEEEES-TT-HHHHHHHHTT..-EEEEEEE--TTTHHHHHHH-..-SEEEES-TTTS-GS--...-SEEEE---GGGTECTSE.E- CS DNA_methylase 1 lkfidLfaGiGGfrlgleaag..fecvaaseidkkaaktYeanfk.kvsigDitkidkkklpe.d.iDlLvgGfPCqpfSvaGk.qk 81 +++++Lf+GiG ++l++ g + + +aseid+ a+ + +++++ + gD+tk+++++++ +DlL+gG PC++ S a +k tr|H2YJ39|H2YJ39_CIOSA 11 IRVLSLFDGIGTGLVALKQLGlqIGMFVASEIDEAAIRLVQNRHPeVIHVGDVTKFSDDDVRRlGpFDLLIGGSPCNDLSGANPrRK 97 5899*****************988999******************77788*********7776535**************9986488 PP -TTSGGG..HHHHHHHHHHHHH-............-SEEEEEEEGGGG CS DNA_methylase 82 gfedtrg..tLffeiiriikekk............PkvfllENVkgLl 115 g d g Lff++ ri+++ + P + l+ENV ++ tr|H2YJ39|H2YJ39_CIOSA 98 GLLDSDGtgCLFFDFYRILRAAEpprcecnagksrPFFWLFENVLSMK 145 9988888668*************7777777777778888888887665 PP == domain 2 score: -0.1 bits; conditional E-value: 0.16 -B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-- CS DNA_methylase 259 klekelaeagklqknkerfkpviekkriRrLtprEaarlqGfPddfe 305 kl++ +++ g l + r pv + ++ L E+ r+ G+P+ ++ tr|H2YJ39|H2YJ39_CIOSA 213 KLNTITTKPGCLYQGHTRIAPVTHMGKEDILWSTELERIFGLPKHYT 259 5566666667777777777778888888899999*********9986 PP >> tr|H2ZR26|H2ZR26_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 53.1 0.0 1e-17 2e-14 1 115 [. 341 472 .. 341 485 .. 0.85 2 ! 8.4 0.0 0.00041 0.79 286 332 .. 574 622 .. 533 625 .. 0.81 Alignments for each domain: == domain 1 score: 53.1 bits; conditional E-value: 1e-17 -EEEEES-TT-HHHHHHHHTT..-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-GS--...-SEEEE---GGGTECTS.EE CS DNA_methylase 1 lkfidLfaGiGGfrlgleaag..fecvaaseidkkaaktYeanfk..kvsigDitkidkkklpe.d.iDlLvgGfPCqpfSvaG.kq 80 +k+++Lf+Gi ++l++ g +e+++aseid +a+ + e +++ ++ gD +i++k l + +Dl++gG PC++ S+ ++ tr|H2ZR26|H2ZR26_CIOSA 341 MKVLSLFDGISTGFVSLQQLGinVEVYFASEIDHEAICVSEIRHPmhIKHVGDACEITDKMLGDwGpFDLVIGGSPCNDLSIVNpAR 427 799******************999*********************999999*********8876536**************986258 PP --TTSGGG..HHHHHHHHHHHHH-........-SEEEEEEEGGGG CS DNA_methylase 81 kgfedtrg..tLffeiiriikekk........PkvfllENVkgLl 115 kg+ ++g Lffe++ri++ k + l+ENV + tr|H2ZR26|H2ZR26_CIOSA 428 KGIWSDKGsgHLFFEYVRILNTCKllaasnqrSLFWLFENVVCMD 472 8986666656**********9988777777778888888886654 PP == domain 2 score: 8.4 bits; conditional E-value: 0.00041 --B-BHHHHHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHHHH CS DNA_methylase 286 iRrLtprEaarlqGfPddfefgskks..aaykqiGnsVpvpvieaiake 332 + L E r+ GfPd ++ + + +++G s +vpvi++++ tr|H2ZR26|H2ZR26_CIOSA 574 HDCLWITEIERVFGFPDHYTDVCNLPrsGRLRVLGKSWSVPVIKHLFTP 622 55577789***********97777666599***************9875 PP >> tr|H2Y5Z0|H2Y5Z0_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.9 0.0 1.1e-06 0.0021 3 44 .. 134 178 .. 133 231 .. 0.78 Alignments for each domain: == domain 1 score: 16.9 bits; conditional E-value: 1.1e-06 EEEES-TT-HHHHHHH.HTT-EEEEEEE--TTTHHHHHHH-...- CS DNA_methylase 3 fidLfaGiGGfrlgle.aagfecvaaseidkkaaktYeanfk..k 44 ++dLfaGiG f+l l a+ e v a e++++a++ + +n++ k tr|H2Y5Z0|H2Y5Z0_CIOSA 134 VVDLFAGIGYFTLPLLvHAKAEFVHACEWNPDAVDALTRNIHdnK 178 79***********9751667********************98652 PP >> tr|H2ZQD2|H2ZQD2_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.8 0.1 3.7e-05 0.072 3 90 .. 52 150 .. 51 164 .. 0.75 Alignments for each domain: == domain 1 score: 11.8 bits; conditional E-value: 3.7e-05 EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.........-SEEEES-TTTS-..GS--..-SEEEE---GGGTECTS CS DNA_methylase 3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk........kvsigDitkidkk..klpe.diDlLvgGfPCqpfSvaG 78 + dL +G+G +++g + g + ++ ++idk+a ++ n + + ++ D+ k++ l++ ++D ++ +P S G tr|H2ZQD2|H2ZQD2_CIOSA 52 VCDLGCGCGILSIGSSILGASYCLGVDIDKEALGIFLSNCEdyelestvDCVHSDVVKLASCrnVLRKkQFDTVIMNPPFGTKSNKG 138 689*********************************999987765544444455555555446666665688887777777777777 PP EE--TTSGGGHH CS DNA_methylase 79 kqkgfedtrgtL 90 +f + ++L tr|H2ZQD2|H2ZQD2_CIOSA 139 IDMDFLKAASQL 150 666666666655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (335 nodes) Target sequences: 11592 (4231397 residues searched) Passed MSV filter: 949 (0.0818668); expected 231.8 (0.02) Passed bias filter: 371 (0.0320048); expected 231.8 (0.02) Passed Vit filter: 43 (0.00370945); expected 11.6 (0.001) Passed Fwd filter: 7 (0.000603865); expected 0.1 (1e-05) Initial search space (Z): 11592 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 0.18u 0.01s 00:00:00.19 Elapsed: 00:00:00.06 # Mc/sec: 23625.30 // [ok]