# 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/Petromyzon_marinus.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
3.6e-34 118.2 0.0 1.1e-33 116.6 0.0 1.8 1 tr|S4RCC7|S4RCC7_PETMA Uncharacterized protein OS=Petromyzon
3.9e-15 55.6 0.0 1.9e-12 46.8 0.0 2.1 2 tr|S4RQV8|S4RQV8_PETMA DNA methyltransferase 3 alpha OS=Petr
2.8e-13 49.5 0.0 4.9e-13 48.7 0.0 1.4 1 tr|S4RTF0|S4RTF0_PETMA DNA methyltransferase 3 alpha OS=Petr
3e-13 49.4 0.0 5.2e-13 48.6 0.0 1.4 1 tr|S4RTE7|S4RTE7_PETMA DNA methyltransferase 3 alpha OS=Petr
1.6e-06 27.3 0.0 1.8e-06 27.2 0.0 1.0 1 tr|S4RQW1|S4RQW1_PETMA DNA methyltransferase 3 alpha OS=Petr
------ inclusion threshold ------
0.12 11.2 0.0 0.18 10.7 0.0 1.1 1 tr|S4RY85|S4RY85_PETMA Electron transfer flavoprotein subuni
Domain annotation for each sequence (and alignments):
>> tr|S4RCC7|S4RCC7_PETMA Uncharacterized protein OS=Petromyzon marinus OX=7757 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 116.6 0.0 4.8e-37 1.1e-33 2 335 .] 66 522 .. 65 522 .. 0.72
Alignments for each domain:
== domain 1 score: 116.6 bits; conditional E-value: 4.8e-37
EEEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-............GS--...-SEEEE---G CS
DNA_methylase 2 kfidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk..kvsigDitkidkk............klpe..diDlLvgGfPC 71
+ +d f+G+GG++ g+++ag +e+ +a+e+++ aa+ ++ n++ v ++D + + k lp+ d++lL+gG+PC
tr|S4RCC7|S4RCC7_PETMA 66 RGLDVFSGCGGLSEGFHQAGiTETKWAIEMWEPAAQAFRLNNPgsTVFTEDCNILLKLvmsgektnglgqRLPQkgDVELLCGGPPC 152
678*****************99**********************755666766665557778888999999998667********** PP
GGTECTSE..E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGG.GGCCS..HHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB-- CS
DNA_methylase 72 qpfSvaGk..qkgfedtrgtLffeiiriikekkPkvfllENVkgLl.khdkg..ktlkvilekleelGYevsykllnasdyGvpQnR 153
q+fS ++ +++L + + + + P+++l V +L + + g k lk+ l +l +++ + l a +yGv+Q R
tr|S4RCC7|S4RCC7_PETMA 153 QGFSGMNRfnSRTYSMFKNSLVVSYLSLMYFYCPNFVLC-QVLMLYfDFQAGmeKLLKITWLCLGSLKQSCNCSFLVAGQYGVAQTR 238
****776543555555666***************98776.5888862444447699999999************************* PP
EEEEEEEEEGGG---........................-------SS---GGG.....TSGGGTTS-EEBTTTB--GGGSSSTT-E CS
DNA_methylase 154 eRvfivgirkdleln........................vlvkvkefrfpkkkdleasktlrdlleekseldeektalsdklvekee 216
+R +i++ +++l + ++v++ ++ + ++++t+ dl+e + + + + +++e
tr|S4RCC7|S4RCC7_PETMA 239 RRAIILAAAPGEKLPfypaplhvfapracqlsvvvgdkkYVSNVTKVSSAPFRTITVRDTMSDLPEIR-----NGASALEISYNSEP 320
**********9988788866666666666655554444433333333333333344445555555432.....22222222222223 PP
E--.......S---HHHTS--.................................B--TTS...-B----S-STT-............ CS
DNA_methylase 217 kikkttkaseegypkelsrnr.................................idkveelkglsatrrksgrge............ 258
+++ +++ + +y+ + r+ + ++ +k+l+ t+++ ++g+
tr|S4RCC7|S4RCC7_PETMA 321 QSWFQRQIRGMQYQ-PILRDHickdlsplvearmryiplapgsdwrdlpnievrLSDGTTSKILRYTHHDRKNGRgsamlrgvcscs 406
33333333333333.222222555556666777789999999999999998888555555555555555555555668888877777 PP
...........................................-B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--T CS
DNA_methylase 259 ...........................................klekelaeagklqknkerfkpviekkriRrLtprEaarlqGfPd 302
++ +++ ++++k+++ v++++++R ++rE+ar qGfPd
tr|S4RCC7|S4RCC7_PETMA 407 evagkpcdsadrqfntlipwclphtgnrhnhwaglygrlewdgFFSTTVTNPEPMGKQGR----VLHPEQHRVVSVRECARSQGFPD 489
777777777777666666666666666666666666655555555555555566666666....9********************** PP
T-----SBHHHHHHHHTS--HHHHHHHHHHHHH CS
DNA_methylase 303 dfefgskksaaykqiGnsVpvpvieaiakeikk 335
++ + +++ ++ +q+Gn+Vp+p+++ai+ eikk
tr|S4RCC7|S4RCC7_PETMA 490 TYRLFGNTLDKHRQVGNAVPPPLAKAIGLEIKK 522
****************************99986 PP
>> tr|S4RQV8|S4RQV8_PETMA DNA methyltransferase 3 alpha OS=Petromyzon marinus OX=7757 GN=DNMT3A (1 of many) PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 46.8 0.0 8.3e-16 1.9e-12 1 120 [. 203 337 .. 203 351 .. 0.84
2 ! 6.8 0.0 0.0012 2.8 295 332 .. 372 411 .. 369 414 .. 0.90
Alignments for each domain:
== domain 1 score: 46.8 bits; conditional E-value: 8.3e-16
-EEEEES-TT-HHHHHHHHTT..-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-GS--...-SEEEE---GGGTECTSE.E CS
DNA_methylase 1 lkfidLfaGiGGfrlgleaag..fecvaaseidkkaaktYeanfk..kvsigDitkidkkklpe.d.iDlLvgGfPCqpfSvaGk.q 80
+++++Lf+Gi l l+ g e ++asei ++ + + +++ + gDi++++ k + e +Dl++gG PC++ S+ +
tr|S4RQV8|S4RQV8_PETMA 203 IRVLSLFDGIATGLLVLKDLGikLERYVASEICEDSIVVGTVRHEgkITYVGDIRNLTRKHILEwGpFDLVIGGSPCNDLSIVNPaR 289
5899*****************99999********98888888888779999*********7776536**************987536 PP
--.TTSGGGHHHHHHHHHHHHH-.......-SEEEEEEEGGGGGGCCS CS
DNA_methylase 81 kg.fedtrgtLffeiiriikekk.......PkvfllENVkgLlkhdkg 120
kg ++ g Lffe+ r++ e k P + l+ENV + +dk+
tr|S4RQV8|S4RQV8_PETMA 290 KGlYAEGTGRLFFEFYRLLHEAKpkegedrPFFWLFENVAAMGVNDKR 337
662577888**************5555555568899***998777765 PP
== domain 2 score: 6.8 bits; conditional E-value: 0.0012
HHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHHHH CS
DNA_methylase 295 arlqGfPddfefgskks..aaykqiGnsVpvpvieaiake 332
r+ GfP ++ s+ s a+ +++G s +vpvi++++
tr|S4RQV8|S4RQV8_PETMA 372 NRIFGFPVHYTDVSNMSrlARQRLLGRSWSVPVIRHLFSP 411
69*********999999889999*************9875 PP
>> tr|S4RTF0|S4RTF0_PETMA DNA methyltransferase 3 alpha OS=Petromyzon marinus OX=7757 GN=DNMT3A (1 of many) PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 48.7 0.0 2.2e-16 4.9e-13 1 120 [. 346 479 .. 346 493 .. 0.90
Alignments for each domain:
== domain 1 score: 48.7 bits; conditional E-value: 2.2e-16
-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 l++ g +e ++ase ++ +++ ++ + igDi++++ ++l++ +Dl++gG PC + S+ ++
tr|S4RTF0|S4RTF0_PETMA 346 IKVLSLFDGIATGLLVLKELGirVERYVASEVCQDSINVGTVRHAgdITYIGDIRNLTYSNLQKwGpFDLVIGGSPCSDLSIVNpAR 432
689******************999********************9999************9998757**************98736* PP
--TTSGGGHHHHHHHHHHHHH--S.......EEEEEEEGGGGGGCCS CS
DNA_methylase 81 kgfedtrgtLffeiiriikekkPk.......vfllENVkgLlkhdkg 120
kg + g Lffe+ r+ +e kP + l+ENV + ++dk+
tr|S4RTF0|S4RTF0_PETMA 433 KGLYEGTGRLFFEFYRLMNEAKPRegeerifFWLFENVAAMGNNDKR 479
**********************9666666545589******999987 PP
>> tr|S4RTE7|S4RTE7_PETMA DNA methyltransferase 3 alpha OS=Petromyzon marinus OX=7757 GN=DNMT3A (1 of many) PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 48.6 0.0 2.3e-16 5.2e-13 1 120 [. 364 497 .. 364 511 .. 0.90
Alignments for each domain:
== domain 1 score: 48.6 bits; conditional E-value: 2.3e-16
-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 l++ g +e ++ase ++ +++ ++ + igDi++++ ++l++ +Dl++gG PC + S+ ++
tr|S4RTE7|S4RTE7_PETMA 364 IKVLSLFDGIATGLLVLKELGirVERYVASEVCQDSINVGTVRHAgdITYIGDIRNLTYSNLQKwGpFDLVIGGSPCSDLSIVNpAR 450
689******************999********************9999************9998757**************98736* PP
--TTSGGGHHHHHHHHHHHHH--S.......EEEEEEEGGGGGGCCS CS
DNA_methylase 81 kgfedtrgtLffeiiriikekkPk.......vfllENVkgLlkhdkg 120
kg + g Lffe+ r+ +e kP + l+ENV + ++dk+
tr|S4RTE7|S4RTE7_PETMA 451 KGLYEGTGRLFFEFYRLMNEAKPRegeerifFWLFENVAAMGNNDKR 497
**********************9666666545589*****9999987 PP
>> tr|S4RQW1|S4RQW1_PETMA DNA methyltransferase 3 alpha OS=Petromyzon marinus OX=7757 GN=DNMT3A (1 of many) PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 27.2 0.0 7.9e-10 1.8e-06 47 103 .. 3 63 .. 1 65 [. 0.82
Alignments for each domain:
== domain 1 score: 27.2 bits; conditional E-value: 7.9e-10
EEES-TTTS-GS--...-SEEEE---GGGTECTSE.E--.TTSGGGHHHHHHHHHHHHH-- CS
DNA_methylase 47 igDitkidkkklpe.d.iDlLvgGfPCqpfSvaGk.qkg.fedtrgtLffeiiriikekkP 103
gDi++++ k + e +Dl++gG PC++ S+ +kg ++ g Lffe+ r++ +P
tr|S4RQW1|S4RQW1_PETMA 3 VGDIRNLTRKHILEwGpFDLVIGGSPCNDLSIVNPaRKGlYAEGTGRLFFEFYRLLMRPSP 63
59********7776536**************987536662577888*********987776 PP
>> tr|S4RY85|S4RY85_PETMA Electron transfer flavoprotein subunit beta lysine methyltransferase OS=Petromyzon marinus OX
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 10.7 0.0 8e-05 0.18 3 34 .. 73 104 .. 72 113 .. 0.92
Alignments for each domain:
== domain 1 score: 10.7 bits; conditional E-value: 8e-05
EEEES-TT-HHHHHHHHTT-EEEEEEE--TTT CS
DNA_methylase 3 fidLfaGiGGfrlgleaagfecvaaseidkka 34
++dL +G+G+ +++ ++ag + v+a++id+ a
tr|S4RY85|S4RY85_PETMA 73 VLDLGSGCGAAAIAAAKAGASLVVANDIDPGA 104
78***************************987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (335 nodes)
Target sequences: 13539 (5048892 residues searched)
Passed MSV filter: 626 (0.0462368); expected 270.8 (0.02)
Passed bias filter: 342 (0.0252604); expected 270.8 (0.02)
Passed Vit filter: 38 (0.00280671); expected 13.5 (0.001)
Passed Fwd filter: 7 (0.000517025); expected 0.1 (1e-05)
Initial search space (Z): 13539 [actual number of targets]
Domain search space (domZ): 6 [number of targets reported over threshold]
# CPU time: 0.19u 0.01s 00:00:00.20 Elapsed: 00:00:00.06
# Mc/sec: 28189.65
//
[ok]