# 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/Strongylocentrotus_purpuratus.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.3e-50 172.5 0.0 2.3e-50 172.5 0.0 2.9 2 tr|W4Z639|W4Z639_STRPU DNA (cytosine-5)-methyltransferase OS
4.1e-24 86.2 1.9 2.9e-18 67.0 0.0 3.5 4 tr|W4Z875|W4Z875_STRPU Uncharacterized protein OS=Strongyloc
6.3e-15 56.0 22.0 3.8e-11 43.6 6.5 2.9 3 tr|W4YG42|W4YG42_STRPU Uncharacterized protein OS=Strongyloc
1.2e-14 55.1 0.0 1.4e-14 54.9 0.0 1.1 1 tr|W4YMI6|W4YMI6_STRPU Uncharacterized protein OS=Strongyloc
------ inclusion threshold ------
0.021 14.9 0.5 0.026 14.5 0.5 1.1 1 tr|W4Z8R0|W4Z8R0_STRPU Uncharacterized protein OS=Strongyloc
0.067 13.2 0.0 0.12 12.4 0.0 1.3 1 tr|W4ZG91|W4ZG91_STRPU Uncharacterized protein OS=Strongyloc
0.18 11.8 0.0 0.29 11.1 0.0 1.3 1 tr|W4YQG0|W4YQG0_STRPU Uncharacterized protein OS=Strongyloc
Domain annotation for each sequence (and alignments):
>> tr|W4Z639|W4Z639_STRPU DNA (cytosine-5)-methyltransferase OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -15.8 17.3 7 2.9e+04 186 196 .. 189 199 .. 37 349 .. 0.58
2 ! 172.5 0.0 5.6e-54 2.3e-50 2 334 .. 1138 1590 .. 1137 1591 .. 0.79
Alignments for each domain:
== domain 1 score: -15.8 bits; conditional E-value: 7
...TSGGGTTS CS
DNA_methylase 186 asktlrdllee 196
++k+l d + e
tr|W4Z639|W4Z639_STRPU 189 KRKVLGDSDRE 199
23333333333 PP
== domain 2 score: 172.5 bits; conditional E-value: 5.6e-54
EEEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-...............-SEEEES-TTTS-GS--...-SEEEE-- CS
DNA_methylase 2 kfidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk..............kvsigDitkidkkklpe..diDlLvgGf 69
k++d faG+GG++ g+++ag e +a+e+++ aa+ ++ n++ v +gD t + +klp+ d++lL+gG+
tr|W4Z639|W4Z639_STRPU 1138 KCLDVFAGCGGLSEGFHQAGiCESSWAIEKEEPAAQAFRLNNPgstvfsddcnellrLVMQGDKTSRTGQKLPQkgDVELLCGGP 1222
899*****************99**********************87777766666655667777777777***9766******** PP
-GGGTECTSE..E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB- CS
DNA_methylase 70 PCqpfSvaGk..qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnasdyGvpQn 152
PCq+fS ++ + +++L+ + + + ++P +fllENV++ ++ +k+ +lk l l +GY++++ +l+a +yGvpQ
tr|W4Z639|W4Z639_STRPU 1223 PCQGFSGMNRfnSREYSKFKNSLISSYLSYCDYYRPRFFLLENVRNFVSYKKNMVLKLALRCLIRMGYQCTFGILQAGQYGVPQT 1307
******988754666677778**************************************************************** PP
-EEEEEEEEEGGG---...............-------SS---GGG..............TSGGGTTS-EE.BTTTB--GGGSSS CS
DNA_methylase 153 ReRvfivgirkdleln...............vlvkvkefrfpkkkd.........leasktlrdlleekse.ldeektalsdklv 212
R+R +i++ +++l ++v + +++ +++++ ++++ + dl++ + + ++ + +++ +
tr|W4Z639|W4Z639_STRPU 1308 RRRAIILAAAPGEKLPfypeplhvfspracsLSVMIGDKKIQSNNQwclsapyrtISVRDSMSDLPTIS-NgAQKLEISYDGEPQ 1391
***********9988898988888888887755555566665555577777544433344444444432.223333333333333 PP
TT-EE--.......S---HHHTS--.................................B--TTS...-B----S-STT-...... CS
DNA_methylase 213 ekeekikkttkaseegypkelsrnr.................................idkveelkglsatrrksgrge...... 258
++ +k+ +++y++ + r+ ++++ +++l+ t+r++++g+
tr|W4Z639|W4Z639_STRPU 1392 SDFQKK-----IRGNQYQP-ILRDHmckdmsalvaarmkhiplapgsdwrdlpnipvpLKDGTTCRKLRYTHRDTKSGKlstgal 1470
333333.....33444443.22222355557777888899999999999999999999888888899999999988888888888 PP
................................................-B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHH CS
DNA_methylase 259 ................................................klekelaeagklqknkerfkpviekkriRrLtprEaa 295
++ +++ ++++k+++ v++++++R ++rE+a
tr|W4Z639|W4Z639_STRPU 1471 kgvcscaegeacdpsdrqfstlipwclphtgnrhnhwaglygrlewdgFFSTTVTNPEPMGKQGR----VLHPEQHRVVSVRECA 1551
88888888888888888777777777777777777777777766666555556666666666666....9*************** PP
HHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHHH CS
DNA_methylase 296 rlqGfPddfefgskksaaykqiGnsVpvpvieaiakeik 334
r qGfPd++ f ++ ++ +q+Gn+Vp+p++ ai+ eik
tr|W4Z639|W4Z639_STRPU 1552 RSQGFPDTYRFFGSILDKHRQVGNAVPPPMAAAIGMEIK 1590
***********************************9997 PP
>> tr|W4Z875|W4Z875_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -3.9 0.1 2.5 1e+04 184 214 .. 251 281 .. 190 316 .. 0.48
2 ? 0.1 0.7 0.16 6.4e+02 186 249 .. 465 529 .. 443 648 .. 0.60
3 ! 67.0 0.0 7.2e-22 2.9e-18 1 119 [. 1184 1316 .. 1184 1324 .. 0.92
4 ! 15.6 0.0 3e-06 0.012 260 331 .. 1382 1455 .. 1349 1459 .. 0.82
Alignments for each domain:
== domain 1 score: -3.9 bits; conditional E-value: 2.5
.....TSGGGTTS-EEBTTTB--GGGSSSTT CS
DNA_methylase 184 leasktlrdlleekseldeektalsdklvek 214
l +k+lr++++e+ + ++++++ +
tr|W4Z875|W4Z875_STRPU 251 LCPRKILRKMEQEEASAGVPGNFIQEEWLTQ 281
2222333333333322333333333333333 PP
== domain 2 score: 0.1 bits; conditional E-value: 0.16
...TSGGGTTS-EE....BTTTB--GGGSSSTT-EE--.......S---HHHTS--B--TTS...-B- CS
DNA_methylase 186 asktlrdlleekse....ldeektalsdklvekeekikkttkaseegypkelsrnridkveelkglsa 249
+++ +++ + + s+ ++ +l+ ++v ++e +++ +++s g +++l+++ +kv++ k +s+
tr|W4Z875|W4Z875_STRPU 465 KTPKVKKHKHK-SPhknkRTSSARRLDMQHVGDKEASHDDKESSPPGTKDKLHKK--RKVKKNKHKSH 529
22222222222.1101111111112222222222222222222222222233333..22222222222 PP
== domain 3 score: 67.0 bits; conditional E-value: 7.2e-22
-EEEEES-TT-HHHHHHHHTT..-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-GS--...-SEEEE---GGGTECTS. CS
DNA_methylase 1 lkfidLfaGiGGfrlgleaag..fecvaaseidkkaaktYeanfk..kvsigDitkidkkklpe.d.iDlLvgGfPCqpfSvaG. 78
+++++Lf+G+G l l++ g +ec++ase ++a+++ + + k ++igD++ki+ k+l+ +D+L+gG PC++ S+
tr|W4Z875|W4Z875_STRPU 1184 IRVLSLFDGLGTGMLVLRELGfdVECYYASEVSEEAITVAAVRLKgqIQQIGDVQKITPKELKSwGpFDILIGGSPCNDLSIVNp 1268
5899*****************999*****************99999999**************8747**************9873 PP
EE--TTSGGGHHHHHHHHHHHHH-.......-SEEEEEEEGGGGGGCC CS
DNA_methylase 79 kqkgfedtrgtLffeiiriikekk.......PkvfllENVkgLlkhdk 119
++kg + g Lffe+ ri+++ + P + l+ENV + +dk
tr|W4Z875|W4Z875_STRPU 1269 ARKGLAGGTGLLFFEFYRILRDLQplpddprPFFWLFENVVFMGRKDK 1316
6***********************888888888999****98887776 PP
== domain 4 score: 15.6 bits; conditional E-value: 3e-06
B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHHH CS
DNA_methylase 260 lekelaeagklqknkerfkpviekkriRrLtprEaarlqGfPddfefgskks..aaykqiGnsVpvpvieaiak 331
+ + ++++ + +++k pvi + r+ L E+ rl GfPd ++ ++ s a+ k++G + +vpvi++++
tr|W4Z875|W4Z875_STRPU 1382 VGTITTTSHSIRQTKDAILPVIMNGREDGLWSTELERLFGFPDHYTDVGNLSrtARQKLLGKAWSVPVIRHLMA 1455
44455556666666666666999999999*****************99988888999*************9976 PP
>> tr|W4YG42|W4YG42_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 2.1 0.1 0.039 1.6e+02 1 17 [. 20 36 .. 20 39 .. 0.88
2 ! 43.6 6.5 9.2e-15 3.8e-11 78 254 .. 39 240 .. 36 269 .. 0.62
3 ! 18.6 4.0 3.8e-07 0.0016 123 254 .. 286 443 .. 259 464 .. 0.56
Alignments for each domain:
== domain 1 score: 2.1 bits; conditional E-value: 0.039
-EEEEES-TT-HHHHHH CS
DNA_methylase 1 lkfidLfaGiGGfrlgl 17
l+++++f+G+GG++ +
tr|W4YG42|W4YG42_STRPU 20 LRVVEFFSGVGGLHCAV 36
589**********9876 PP
== domain 2 score: 43.6 bits; conditional E-value: 9.2e-15
SEE--TTSGGGHHHHHHHHHHHH..H--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB--EEEEEEEEE CS
DNA_methylase 78 GkqkgfedtrgtLffeiiriike..kkPkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnasdyGvpQnReRvfivgir 162
G + + +d r + ff+i+r + e kkP+++l ENVkg ++ +t + ++e+l++++Y ++ ll ++G+p +R R f+++ +
tr|W4YG42|W4YG42_STRPU 39 GLKGDKNDARTNAFFNIMRNLAEmaKKPTYLLVENVKGFDTS---ETRNFLVETLQKCNYVFQEFLLSPMNIGIPNQRVRYFMLAKQ 122
77788999*************974478***********9888...6788899*********************************** PP
GGG---...........-------SS---GGG.....................TSGGGTTS-EE.....BTTTB--GGGSSSTT-EE CS
DNA_methylase 163 kdleln...........vlvkvkefrfpkkkd................leasktlrdlleekse.....ldeektalsdklvekeek 217
+l+ + v +++ ++ ++ ++ + + ++ r + + ++ ++++k+ e++
tr|W4YG42|W4YG42_STRPU 123 RPLQFKeehgtqlvqhrVNMPLMPNEIKETSRlvcdnsmvssqeqtnmELTESRERTG-----QdessmVSLNEQSIERKTDEQHLN 204
**99888877776555544444444444444455555544433222221111111111.....112222333333333333333333 PP
--.......S---HHHTS--B--TTS...-B----S- CS
DNA_methylase 218 ikkttkaseegypkelsrnridkveelkglsatrrks 254
k++t + ++g + ++++ ++ e+ g+ + rrk+
tr|W4YG42|W4YG42_STRPU 205 EKERTDNVKSGSCEDMVSS-SEQNEQETGEDDERRKI 240
3332222222222122222.34444444444444444 PP
== domain 3 score: 18.6 bits; conditional E-value: 3.8e-07
HHHHHHHHHHHTEEEEEEEEEGGGTT-SB--EEEEEEEEEGGG---...........-------SS---GGG............... CS
DNA_methylase 123 lkvilekleelGYevsykllnasdyGvpQnReRvfivgirkdleln...........vlvkvkefrfpkkkd............... 183
+ ++e+l++++Y ++ ll ++G+p +R R f+++ + +l+ + v +++ ++ ++ ++
tr|W4YG42|W4YG42_STRPU 286 ANFLVETLQKCNYVFQEFLLSPMNIGIPNQRVRYFMLAKQRPLQFKeehgtqlvqhrVNMPLMPNEIKETSRlvcdnsmvssqeqtn 372
466789************************************998888776665555444444444444444554445444332222 PP
......TSGGGTTS-EE.....BTTTB--GGGSSSTT-EE--.......S---HHHTS--B--TTS...-B----S- CS
DNA_methylase 184 .leasktlrdlleekse.....ldeektalsdklvekeekikkttkaseegypkelsrnridkveelkglsatrrks 254
+ + ++ r + + ++ ++++k+ e++ k++t + ++g + ++++ ++ e+ g+ + rrk+
tr|W4YG42|W4YG42_STRPU 373 mELTESRERTG-----QdessmVSLNEQSIERKTDEQHLNEKERTDNVKSGSCEDMVSS-SEQNEQETGEDDERRKI 443
21111111111.....1112223333333333333333333322222222222122222.34444444444444444 PP
>> tr|W4YMI6|W4YMI6_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 54.9 0.0 3.5e-18 1.4e-14 280 334 .. 3 57 .. 1 58 [. 0.96
Alignments for each domain:
== domain 1 score: 54.9 bits; conditional E-value: 3.5e-18
.TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHHH CS
DNA_methylase 280 viekkriRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakeik 334
v++++++R ++rE+ar qGfPd++ f ++ ++ +qiGn+Vp+p++ ai+ eik
tr|W4YMI6|W4YMI6_STRPU 3 VLHPEQHRVVSVRECARSQGFPDTYRFFGSILDKHRQIGNAVPPPMAAAIGMEIK 57
689************************************************9997 PP
>> tr|W4Z8R0|W4Z8R0_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 14.5 0.5 6.5e-06 0.026 133 272 .. 7 158 .. 3 169 .. 0.55
Alignments for each domain:
== domain 1 score: 14.5 bits; conditional E-value: 6.5e-06
HTEEEEEEEEEGGGTT-SB--EEEEEEEEEGGG---..-------SS---GGG........TSGGGTTS-EEBTTTB--GGGSSSTT CS
DNA_methylase 133 lGYevsykllnasdyGvpQnReRvfivgirkdleln..vlvkvkefrfpkkkd...leasktlrdlleekseldeektalsdklvek 214
++Y ++ + a+d+ p nReR+ v++r + l+++++++fp +s+++ ++l+ + + e t+l + ve
tr|W4Z8R0|W4Z8R0_STRPU 7 IDYLNHNFVTWAWDMTSPKNRERLLAVCTRIFGSVTasTLKNLQQDKFPLLLLamrIRSSTEVFSVLQGNLSHGELLTSLM-QAVEF 92
56888888999******************9765554558888888888888656664445555555554433333333333.45566 PP
-EE--.......S---H.HHTS--B--TTS...-B----S-STT-.......-B-TTS---EEEET CS
DNA_methylase 215 eekikkttkaseegypk.elsrnridkveelkglsatrrksgrge.......klekelaeagklqk 272
e+ + +++ +eeg + e+ + +d+ ++ +++ ++ ++ + +++ke ++ +++ +
tr|W4Z8R0|W4Z8R0_STRPU 93 FETQQHANVVQEEGRRAsEMLKMEQDQAYQESLIVDRAKQEEKERqereegaRIMKEQQDEQMKKE 158
666666666666666654333333333333222222222222211112222244444444444433 PP
>> tr|W4ZG91|W4ZG91_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.4 0.0 2.9e-05 0.12 3 43 .. 23 64 .. 22 78 .. 0.88
Alignments for each domain:
== domain 1 score: 12.4 bits; conditional E-value: 2.9e-05
EEEES-TT-HHHHH.HHHTT-EEEEEEE--TTTHHHHHHH-. CS
DNA_methylase 3 fidLfaGiGGfrlg.leaagfecvaaseidkkaaktYeanfk 43
++dL aGiG f+l l a+ + +a e++++a+k +++n k
tr|W4ZG91|W4ZG91_STRPU 23 VVDLYAGIGYFTLPyLVHAKAKLLYACEWNPHAVKALRTNLK 64
89***********8577888********************86 PP
>> tr|W4YQG0|W4YQG0_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 11.1 0.0 7e-05 0.29 4 59 .. 53 110 .. 51 126 .. 0.79
Alignments for each domain:
== domain 1 score: 11.1 bits; conditional E-value: 7e-05
EEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-GS- CS
DNA_methylase 4 idLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk..kvsigDitkidkkklp 59
dL +G+G +++g ++ ++ +id++a ++ ++n + + ++ D + d +k++
tr|W4YQG0|W4YQG0_STRPU 53 ADLGCGCGMLSIGAAMLDAGLCIGFDIDQDALEICQRNCEefELPCVDTVQSDLTKME 110
79*************************************9997777776666655443 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (335 nodes)
Target sequences: 28594 (14266044 residues searched)
Passed MSV filter: 2386 (0.0834441); expected 571.9 (0.02)
Passed bias filter: 909 (0.0317899); expected 571.9 (0.02)
Passed Vit filter: 101 (0.00353221); expected 28.6 (0.001)
Passed Fwd filter: 14 (0.000489613); expected 0.3 (1e-05)
Initial search space (Z): 28594 [actual number of targets]
Domain search space (domZ): 7 [number of targets reported over threshold]
# CPU time: 0.59u 0.03s 00:00:00.62 Elapsed: 00:00:00.20
# Mc/sec: 23895.62
//
[ok]