# 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]