# 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/Xenopus_tropicalis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-49 167.1 0.0 3.5e-48 165.1 0.0 2.1 2 tr|F6QE78|F6QE78_XENTR DNA (cytosine-5)-methyltransfera 4.3e-42 145.1 0.0 5.3e-42 144.8 0.0 1.1 1 tr|F6VLZ7|F6VLZ7_XENTR tRNA aspartic acid methyltransfe 5.5e-17 62.5 0.0 3.3e-12 46.8 0.0 2.4 2 tr|F7BU15|F7BU15_XENTR DNA (cytosine-5-)-methyltransfer 0.002 18.0 0.0 0.0038 17.0 0.0 1.4 1 tr|F7AIW5|F7AIW5_XENTR Methyltransferase-like 5 OS=Xeno ------ inclusion threshold ------ 0.15 11.8 0.0 0.2 11.4 0.0 1.1 1 tr|A0A1B8XTI8|A0A1B8XTI8_XENTR Uncharacterized protein OS=Xenop 0.15 11.8 0.0 0.2 11.4 0.0 1.1 1 tr|F6SYY7|F6SYY7_XENTR Uncharacterized protein OS=Xenop Domain annotation for each sequence (and alignments): >> tr|F6QE78|F6QE78_XENTR DNA (cytosine-5)-methyltransferase OS=Xenopus tropicalis OX=8364 GN=dnmt1 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.2 0.5 1.4 5.5e+03 186 226 .. 273 313 .. 243 320 .. 0.59 2 ! 165.1 0.0 8.6e-52 3.5e-48 2 335 .] 1124 1577 .. 1123 1577 .. 0.73 Alignments for each domain: == domain 1 score: -3.2 bits; conditional E-value: 1.4 ...TSGGGTTS-EEBTTTB--GGGSSSTT-EE--....... CS DNA_methylase 186 asktlrdlleekseldeektalsdklvekeekikkttkase 226 + +++ ++++ e+++e+ +++ ++ e+e++++ t ++s+ tr|F6QE78|F6QE78_XENTR 273 KDTDVSADADQPEEKEKEEKRIKIEVNESENENRSTAEESK 313 22223222333334677777777777777777776666555 PP == domain 2 score: 165.1 bits; conditional E-value: 8.6e-52 EEEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-............GS--...-SEEEE-- CS DNA_methylase 2 kfidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk..kvsigDitkidkk............klpe..diDlLvgGf 69 +++d f+G+GG++ g+++ag e+ +a+e+++ aa+ ++ n++ v ++D + + k lp+ d+++L+gG+ tr|F6QE78|F6QE78_XENTR 1124 RTLDVFSGCGGLSEGFHQAGiSETNWAIEMWEPAAQAFRLNNPgtTVFTEDCNVLLKLvmsgektnslgqRLPQkgDVEMLCGGP 1208 789*****************99**********************755555655554445666677889999998667******** PP -GGGTECTSE..E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB- CS DNA_methylase 70 PCqpfSvaGk..qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnasdyGvpQn 152 PCq+fS ++ + +++L + + + + ++Pk+fllENV++ ++ +++ +lk l l +GY++++ +l+a +yGv+Q tr|F6QE78|F6QE78_XENTR 1209 PCQGFSGMNRfnSRTYSKFKNSLVVSYLSYCDYYRPKYFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQT 1293 ******887654666677777**************************************************************** PP -EEEEEEEEEGGG---........................-------SS---GGG.....TSGGGTTS-EEBTTTB--GGGSSST CS DNA_methylase 153 ReRvfivgirkdleln........................vlvkvkefrfpkkkdleasktlrdlleekseldeektalsdklve 213 R+R ++++ +++l + ++++ ++++ + ++++t+ dl+e + + + + ++ tr|F6QE78|F6QE78_XENTR 1294 RRRAIVLAAAPGEKLPmfpeplhvfapracslsvvvdekkYVSNITRTNSSLFRTITVRDTMSDLPEIR-----NGASALEISYN 1373 **********99987777877777777776655555444444444444444443344444444444432.....22222333334 PP T-EE--.......S---HHHTS--.......................................B--TTS...-B----S-STT-. CS DNA_methylase 214 keekikkttkaseegypkelsrnr.......................................idkveelkglsatrrksgrge. 258 e +++ +++ +++y++ + r+ + ++l+ +++++++g+ tr|F6QE78|F6QE78_XENTR 1374 GEPQSWFQRQIRGSQYQP-ILRDHvckdmsalvaarmrhiplapgsdwrdlpnmevrlsdgttT------RKLRYSHHDKKNGRs 1451 444444445555555553.333324666677777888899999999999988888775553332......222222222222224 PP .....................................................-B-TTS---EEEETTEEE--T.TTGGG--B-B CS DNA_methylase 259 .....................................................klekelaeagklqknkerfkpviekkriRrLt 290 ++ +++ ++++k+++ v++++++R + tr|F6QE78|F6QE78_XENTR 1452 stgalrgvcscsegkpcdpadrqfntlipwclphtgnrhnhwaglygrlewdgFFSTTVTNPEPMGKQGR----VLHPEQHRVVS 1532 4566677777777777777777777766666666666666666666666555555555556666666666....9********** PP HHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHHHH CS DNA_methylase 291 prEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakeikk 335 +rE+ar qGfPd++ + ++ ++ +q+Gn+Vp+p+ +ai+ eikk tr|F6QE78|F6QE78_XENTR 1533 VRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLSKAIGSEIKK 1577 ******************************************986 PP >> tr|F6VLZ7|F6VLZ7_XENTR tRNA aspartic acid methyltransferase 1 OS=Xenopus tropicalis OX=8364 GN=trdmt1 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 144.8 0.0 1.3e-45 5.3e-42 2 332 .. 6 390 .. 5 393 .. 0.71 Alignments for each domain: == domain 1 score: 144.8 bits; conditional E-value: 1.3e-45 EEEEES-TT-HHHHHHHHTT..-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-GS--..-SEEEE---GGGTECTSEE--T CS DNA_methylase 2 kfidLfaGiGGfrlgleaag..fecvaaseidkkaaktYeanfk..kvsigDitkidkkklpe.diDlLvgGfPCqpfSvaGkqkgf 83 ++++L +GiGG++ gl + g e+vaa++ + a ++Y+ nf+ + i+ ++ k+l + ++D+++ ++PCqpf G q ++ tr|F6VLZ7|F6VLZ7_XENTR 6 RVLELYSGIGGMHCGLTESGvaAEVVAAVDVNTIANEVYKYNFPytPLWPKSIEGLSLKELDAlSFDMILMSPPCQPFTRIGLQGDI 92 899*****************999*********************8878889999999999*9999********************** PP TSGGGHHHHHHHHHHH..HH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB--EEEEEEEEEGGG--- CS DNA_methylase 84 edtrgtLffeiiriik..ekkPkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnasdyGvpQnReRvfivgirkdleln 168 d+r + f ++ ++ +k+P+++llENVkg +++ + + ++ +le+ GY ++ ll G+p +R R f+++ +++++ tr|F6VLZ7|F6VLZ7_XENTR 93 SDPRTKSFLYVLDVLPrlKKQPAYILLENVKGFETSE---AREALIRTLEKGGYAYQEFLLSPTCLGIPNSRLRYFLIAKLQKEPFA 176 ***************733678************9995...57788**************************************9988 PP .......................-------SS---GGG.....TSGGGTTS-EE..BTTTB--GGGSSSTT-EE--.......S--- CS DNA_methylase 169 .......................vlvkvkefrfpkkkdleasktlrdlleekse..ldeektalsdklvekeekikkttkaseegyp 230 +++ ++ r+++k+ s l+ ++ ++ ++ k e+ + + ++ ++ + tr|F6VLZ7|F6VLZ7_XENTR 177 fpttskileefpsqcpgskriihCSESNPQARVEQKY---------------SScpLSGTDCDPEKTVLYKLETAVELQRKQTQDND 248 8666655555444444444444433444444444443...............33332222222222222222222222222222222 PP H..HHTS--...................................B--TTS...-B----S-STT-......-B-TTS---EEEETTE CS DNA_methylase 231 k..elsrnr...................................idkveelkglsatrrksgrge......klekelaeagklqknk 274 + + +++ +kg+ ++++ +g+ + ++ ++++ l ++ tr|F6VLZ7|F6VLZ7_XENTR 249 SsvRM---LqdflegnveemsqyflppksllryalildivkptcRRSTCFTKGYGHYVEGTGS-VlqtatdVEIDTVYKSLDLLTEE 331 11111...1122233333344445666677666676666666664444444444444444443.13444445555666666666666 PP EE--T.TTGGG--B-BHHHHHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHHHH CS DNA_methylase 275 erfkpviekkriRrLtprEaarlqGfPddfefgskks..aaykqiGnsVpvpvieaiake 332 e+ ++ ++R +tprE l GfP +f f+++ + ++y+++Gns++v ++ ++ tr|F6VLZ7|F6VLZ7_XENTR 332 EKLA-KLSSLKMRYFTPREISNLHGFPATFGFPEEVTkkQRYRLLGNSLNVHIVSCLIST 390 6555.59999***********************998888*************99887766 PP >> tr|F7BU15|F7BU15_XENTR DNA (cytosine-5-)-methyltransferase 3 alpha OS=Xenopus tropicalis OX=8364 GN=dnmt3a 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 3.3e-12 1 120 [. 602 735 .. 602 744 .. 0.88 2 ! 13.2 0.0 1.4e-05 0.054 262 332 .. 800 872 .. 756 875 .. 0.77 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---GGGTECTS.EE CS DNA_methylase 1 lkfidLfaGiGGfrlgleaag..fecvaaseidkkaaktYeanfk..kvsigDitkidkkklpe.d.iDlLvgGfPCqpfSvaG.kq 80 +++++Lf+Gi l l+ g +e ++ase ++ +++ +++ + gD+++i+ k ++e +Dl++gG PC++ S+ ++ tr|F7BU15|F7BU15_XENTR 602 IRVLSLFDGIATGLLVLKDLGihIERYIASEVCEDSITVGMVRHQgkIMYVGDVRNITRKHIQEwGpFDLVIGGSPCNDLSIVNpAR 688 5899*****************99999**********99999999988999**********9998647**************987369 PP --TTSGGGHHHHHHHHHHHHH-.......-SEEEEEEEGGGGGGCCS CS DNA_methylase 81 kgfedtrgtLffeiiriikekk.......PkvfllENVkgLlkhdkg 120 kg + g Lffe+ r++ e + P + l+ENV + +dk+ tr|F7BU15|F7BU15_XENTR 689 KGLFEGTGRLFFEFYRLLHEARpkegdnrPFFWLFENVVAMGVSDKR 735 ********************995555555668899999888776664 PP == domain 2 score: 13.2 bits; conditional E-value: 1.4e-05 TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHHHH CS DNA_methylase 262 kelaeagklqknkerfkpviekkriRrLtprEaarlqGfPddfefgskks..aaykqiGnsVpvpvieaiake 332 + ++++++ + k + pv+ ++++ L E+ r+ GfP ++ s+ s a+ +++G s +vpvi++++ tr|F7BU15|F7BU15_XENTR 800 TITTRSNSIKQGKDQHFPVYMNEKEDILWCTEMERVFGFPVHYTDVSNMSrlARQRLLGRSWSVPVIRHLFAP 872 333333333333333346999999999*****************999999889999*************9875 PP >> tr|F7AIW5|F7AIW5_XENTR Methyltransferase-like 5 OS=Xenopus tropicalis OX=8364 GN=mettl5 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.0 0.0 9.5e-07 0.0038 3 65 .. 55 117 .. 54 129 .. 0.79 Alignments for each domain: == domain 1 score: 17.0 bits; conditional E-value: 9.5e-07 EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTTS-..GS--.-SEE CS DNA_methylase 3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigDitkidkk..klpediDlL 65 + dL +G+G +++g ++ g ++ + d++a +++++n ++ ++ +i+ i+ + +lp D L tr|F7AIW5|F7AIW5_XENTR 55 VADLGCGCGVLSIGAAMLGAGLCLGLDVDEDALDIFKTNTEEFELTNIDMIQFDicSLP--PDCL 117 579**************************************555555555544333666..3544 PP >> tr|A0A1B8XTI8|A0A1B8XTI8_XENTR Uncharacterized protein OS=Xenopus tropicalis OX=8364 GN=etfbkmt PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.4 0.0 4.9e-05 0.2 2 43 .. 103 144 .. 102 163 .. 0.87 Alignments for each domain: == domain 1 score: 11.4 bits; conditional E-value: 4.9e-05 EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-. CS DNA_methylase 2 kfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk 43 +++dL +G+G+ +++ + g + v+a++id+ a + ++ n + tr|A0A1B8XTI8|A0A1B8XTI8_XENTR 103 SVLDLGCGCGAAAIAAGMGGASYVLANDIDPVAGEAFKLNCE 144 589************************************985 PP >> tr|F6SYY7|F6SYY7_XENTR Uncharacterized protein OS=Xenopus tropicalis OX=8364 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.4 0.0 5.1e-05 0.2 2 43 .. 110 151 .. 109 170 .. 0.87 Alignments for each domain: == domain 1 score: 11.4 bits; conditional E-value: 5.1e-05 EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-. CS DNA_methylase 2 kfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk 43 +++dL +G+G+ +++ + g + v+a++id+ a + ++ n + tr|F6SYY7|F6SYY7_XENTR 110 SVLDLGCGCGAAAIAAGMGGASYVLANDIDPVAGEAFKLNCE 151 589************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (335 nodes) Target sequences: 24182 (11782085 residues searched) Passed MSV filter: 1951 (0.0806798); expected 483.6 (0.02) Passed bias filter: 819 (0.0338682); expected 483.6 (0.02) Passed Vit filter: 132 (0.00545861); expected 24.2 (0.001) Passed Fwd filter: 51 (0.00210901); expected 0.2 (1e-05) Initial search space (Z): 24182 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 0.83u 0.03s 00:00:00.86 Elapsed: 00:00:00.33 # Mc/sec: 11960.60 // [ok]