# 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/Anolis_carolinensis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-48 163.7 0.0 3.8e-47 161.3 0.0 2.2 2 tr|H9G8K3|H9G8K3_ANOCA DNA (cytosine-5)-methyltransferase OS 2.1e-41 142.4 0.0 2.6e-41 142.1 0.0 1.1 1 tr|G1KDM2|G1KDM2_ANOCA tRNA aspartic acid methyltransferase 1.2e-16 61.0 0.0 2.7e-12 46.7 0.0 2.3 2 tr|H9GDH4|H9GDH4_ANOCA Uncharacterized protein OS=Anolis car 1.2e-15 57.7 0.0 3.3e-13 49.7 0.0 2.1 2 tr|H9GFQ9|H9GFQ9_ANOCA DNA methyltransferase 3 beta OS=Anoli 0.0011 18.4 0.1 0.0026 17.2 0.0 1.5 2 tr|H9GNU1|H9GNU1_ANOCA Methyltransferase like 5 OS=Anolis ca ------ inclusion threshold ------ 0.027 13.9 2.0 0.033 13.6 2.0 1.1 1 tr|G1KQQ9|G1KQQ9_ANOCA BCL2 interacting protein 1 OS=Anolis Domain annotation for each sequence (and alignments): >> tr|H9G8K3|H9G8K3_ANOCA DNA (cytosine-5)-methyltransferase OS=Anolis carolinensis OX=28377 GN=DNMT1 PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.4 2.2 1.6 5e+03 186 243 .. 216 235 .. 90 297 .. 0.56 2 ! 161.3 0.0 1.2e-50 3.8e-47 2 334 .. 1092 1544 .. 1091 1545 .. 0.74 Alignments for each domain: == domain 1 score: -3.4 bits; conditional E-value: 1.6 ...TSGGGTTS-EEBTTTB--GGGSSSTT-EE--.......S---HHHTS--B--TTS CS DNA_methylase 186 asktlrdlleekseldeektalsdklvekeekikkttkaseegypkelsrnridkvee 243 +++t+ ++++ s+ ++k+ee tr|H9G8K3|H9G8K3_ANOCA 216 KQPTIVAMFSKGSN--------------------------------------KRKSEE 235 22222222222211......................................111111 PP == domain 2 score: 161.3 bits; conditional E-value: 1.2e-50 EEEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-............GS--...-SEEEE-- CS DNA_methylase 2 kfidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk..kvsigDitkidkk............klpe..diDlLvgGf 69 + +d f+G+GG++ g+++a+ e+ +a+e+++ aa+ ++ n++ v ++D + + k klp+ d+++L+gG+ tr|H9G8K3|H9G8K3_ANOCA 1092 RSLDVFSGCGGLSEGFHQAEvSETLWAIEMWEPAAQAFRLNNPgtTVFTEDCNVLLKLvmsgektnslgqKLPQkgDVEMLCGGP 1176 679*****************99**********************755555655554445666677889999998766******** PP -GGGTECTSE..E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB- CS DNA_methylase 70 PCqpfSvaGk..qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnasdyGvpQn 152 PCq+fS ++ + +++L + + + + ++P +fllENV++ ++ +++ +lk l l +GY++++ +l+a +yGv+Q tr|H9G8K3|H9G8K3_ANOCA 1177 PCQGFSGMNRfnSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQT 1261 ******887654666677777**************************************************************** PP -EEEEEEEEEGGG---.................-------SS---GGG..............TSGGGTTS-EEBTTTB--GGGSS CS DNA_methylase 153 ReRvfivgirkdleln.................vlvkvkefrfpkkkd.........leasktlrdlleekseldeektalsdkl 211 R+R ++++ +++l v v +++f ++ ++++t+ dl+e + + + + tr|H9G8K3|H9G8K3_ANOCA 1262 RRRAIVLAAAPGEKLPmfpeplhvfapracqlsV--VVDDKKFVSNITrtysgpfrtITVRDTMSDLPEIR-----NGASALEIS 1339 **********999887889888877777777442..33333333333344666554544455555555542.....222222333 PP STT-EE--.......S---HHHTS--.......................................B--TTS...-B----S-STT CS DNA_methylase 212 vekeekikkttkaseegypkelsrnr.......................................idkveelkglsatrrksgrg 257 ++ e +++ +++ +++y+ + r+ ++k +++ ++++ tr|H9G8K3|H9G8K3_ANOCA 1340 YNGEPQSWFQRQIRGSQYQ-PILRDHickdmsalvaarmrhiplapgsdwrdlpnievrlsdgitTRKLRYTHHEKKNG------ 1417 3444444445555555555.33333345555677777789999999999999999999966655544444444444444...... PP -......................................................-B-TTS---EEEETTEEE--T.TTGGG--B CS DNA_methylase 258 e......................................................klekelaeagklqknkerfkpviekkriRr 288 + ++ +++ ++++k+++ v++++++R tr|H9G8K3|H9G8K3_ANOCA 1418 RsstgalrgvcscaegkacdpadrqfntlipwclphtgnrhnhwaglygrlewdgFFSTTVTNPEPMGKQGR----VLHPEQHRV 1498 344444677777777777777777777766666666666666666666666555545555555555555555....9******** PP -BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHHH CS DNA_methylase 289 LtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakeik 334 ++rE+ar qGfPd++ + ++ ++ +q+Gn+Vp+p+++ai+ eik tr|H9G8K3|H9G8K3_ANOCA 1499 VSVRECARSQGFPDTYRLFGNVLDKHRQVGNAVPPPLAKAIGLEIK 1544 ******************************************9987 PP >> tr|G1KDM2|G1KDM2_ANOCA tRNA aspartic acid methyltransferase 1 OS=Anolis carolinensis OX=28377 GN=TRDMT1 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 142.1 0.0 8.6e-45 2.6e-41 2 331 .. 5 395 .. 4 398 .. 0.79 Alignments for each domain: == domain 1 score: 142.1 bits; conditional E-value: 8.6e-45 EEEEES-TT-HHHHHHHHTT..-EEEEEEE--TTTHHHHHHH-......-SEEEES-TTTS-GS--.-SEEEE---GGGTECTSEE- CS DNA_methylase 2 kfidLfaGiGGfrlgleaag..fecvaaseidkkaaktYeanfk.....kvsigDitkidkkklpediDlLvgGfPCqpfSvaGkqk 81 ++++L +GiGG++++l+a + e+vaa++ + a ++Y nf+ + i++i +++ l+ +++ ++PCqpf G+q+ tr|G1KDM2|G1KDM2_ANOCA 5 RVLELYSGIGGMHYALQASNilAEIVAAVDVNTVANEVYTHNFCttplwPKTIENILLEAINRLRV-QQVILMSPPCQPFTRIGQQR 90 899****************999**********************9999989999999999999996.9******************* PP -TTSGGGHHHHHHHHHHHHH-..-SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB--EEEEEEEEEGGG- CS DNA_methylase 82 gfedtrgtLffeiiriikekk..PkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnasdyGvpQnReRvfivgirkdle 166 + d+r f +i i+ Pk++llENVkg ++ + + ++++ +le++G+ ++ ll G+p R R f+++ ++ ++ tr|G1KDM2|G1KDM2_ANOCA 91 DVSDPRTRSFLYILDILPRLAklPKYLLLENVKGFETSSASTARDELIRTLEKCGFIYQEFLLSPTCLGIPNARLRYFLIARLQTEP 177 *****************876556*************************************************************999 PP --......-------SS---GGG.......................TSGGGTTS-EE......BTTTB--GGGSSSTT-EE--.... CS DNA_methylase 167 ln......vlvkvkefrfpkkkd..................leasktlrdlleekse......ldeektalsdklvekeekikkttk 223 + ++fp++++ l + d++ + +++++ k e+ ++ + tr|G1KDM2|G1KDM2_ANOCA 178 FPfhvpgkI-----LTDFPNQDQvdsersrcstglmeagspLPT------------RetvsgsDDNDGHSSKRDFLFKLETEEELER 247 774322222.....455666655776667776665444333222............1222333344444555555555555555555 PP ...S---H..HHTS--................................B--TTS...-B----S-STT--B-TTS---EEEETTEEE CS DNA_methylase 224 aseegypk..elsrnr................................idkveelkglsatrrksgrgeklekelaeagklqknker 276 +++++ ++ ++ rn +++ +kg+ ++++ +g+ ++ e ++l + + tr|G1KDM2|G1KDM2_ANOCA 248 KQQQDNDPslQMLRNFlqgdgedlsqyllppksllryallldivtpscRRSTCFTKGYGHYIEGTGS----VLQTEEDIQLESVFKS 330 5544444445555555778888888899999999999999999988887777777777777777776....4455555555555555 PP --T.........TTGGG--B-BHHHHHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHHH CS DNA_methylase 277 fkp........viekkriRrLtprEaarlqGfPddfefgskks..aaykqiGnsVpvpvieaiak 331 f++ ++ + R +tprE a l GfP +f f+ k + ++y+++Gns++++v+ +++ tr|G1KDM2|G1KDM2_ANOCA 331 FESlseeeklmKLSLLKLRYFTPREIANLHGFPPEFGFPDKVTtkQQYRLLGNSLNIQVVAKLIS 395 555666677777888999**********************99999***************99875 PP >> tr|H9GDH4|H9GDH4_ANOCA Uncharacterized protein OS=Anolis carolinensis OX=28377 PE=3 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 46.7 0.0 8.8e-16 2.7e-12 1 120 [. 613 746 .. 613 755 .. 0.88 2 ! 12.1 0.0 3e-05 0.094 262 332 .. 811 883 .. 763 886 .. 0.76 Alignments for each domain: == domain 1 score: 46.7 bits; conditional E-value: 8.8e-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 ++ ++ase ++ +++ +++ + gD++++++k ++e +Dl++gG PC++ S+ ++ tr|H9GDH4|H9GDH4_ANOCA 613 IRVLSLFDGIATGLLVLKDLGiqVDRYIASEVCEDSITVGMVRHQgkIMYVGDVRNVTQKHIQEwGpFDLVIGGSPCNDLSIVNpAR 699 5899*****************99999*********9999999999889999*********9998647**************98736* PP --TTSGGGHHHHHHHHHHHHH-.......-SEEEEEEEGGGGGGCCS CS DNA_methylase 81 kgfedtrgtLffeiiriikekk.......PkvfllENVkgLlkhdkg 120 kg + g Lffe+ r++ e + P + l+ENV + +dk+ tr|H9GDH4|H9GDH4_ANOCA 700 KGLYEGTGRLFFEFYRLLHEARpkegderPFFWLFENVVAMGVSDKR 746 *********************95555555568899999888776664 PP == domain 2 score: 12.1 bits; conditional E-value: 3e-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|H9GDH4|H9GDH4_ANOCA 811 TITTRSNSIKQGKDQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSrlARQRLLGRSWSVPVIRHLFAP 883 33333333333333334588899999999***************999999889999*************9875 PP >> tr|H9GFQ9|H9GFQ9_ANOCA DNA methyltransferase 3 beta OS=Anolis carolinensis OX=28377 GN=DNMT3B PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 49.7 0.0 1.1e-16 3.3e-13 1 120 [. 143 276 .. 143 284 .. 0.86 2 ! 6.0 0.0 0.0022 6.8 294 331 .. 310 349 .. 306 353 .. 0.88 Alignments for each domain: == domain 1 score: 49.7 bits; conditional E-value: 1.1e-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 ++asei ++ +++ +++ + +D+++i+k+++ e +Dl++gG PC++ S+ ++ tr|H9GFQ9|H9GFQ9_ANOCA 143 IRVLSLFDGIATGYLVLRDLGikVEKYVASEICEESIAVGTVRHEgnITYVHDVRNITKRNIDEwGpFDLVIGGSPCNDLSIVNpAR 229 5899*****************99999*********88888888877789999*****9999997647**************98736* PP --TTSGGGHHHHHHHHHHHHH-.......-SEEEEEEEGGGGGGCCS CS DNA_methylase 81 kgfedtrgtLffeiiriikekk.......PkvfllENVkgLlkhdkg 120 kg + g Lffe+ +++ + P + l+ENV + +d++ tr|H9GFQ9|H9GFQ9_ANOCA 230 KGLYEGTGRLFFEFYHLLNYSRpkpeeerPFFWLFENVVAMRVNDRR 276 ******************87774444444678999***998877664 PP == domain 2 score: 6.0 bits; conditional E-value: 0.0022 HHHHHT--TT-----SBH..HHHHHHHTS--HHHHHHHHH CS DNA_methylase 294 aarlqGfPddfefgskks..aaykqiGnsVpvpvieaiak 331 + r+ GfP ++ s+ a+ k++G s +vpvi++++ tr|H9GFQ9|H9GFQ9_ANOCA 310 MNRIFGFPLHYTDVSNMGrgARQKLLGRSWSVPVIRHLFA 349 789********998888888*****************986 PP >> tr|H9GNU1|H9GNU1_ANOCA Methyltransferase like 5 OS=Anolis carolinensis OX=28377 GN=METTL5 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.2 0.0 8.5e-07 0.0026 3 70 .. 55 128 .. 54 128 .. 0.88 2 ? -2.3 0.0 0.71 2.2e+03 121 136 .. 170 185 .. 145 200 .. 0.63 Alignments for each domain: == domain 1 score: 17.2 bits; conditional E-value: 8.5e-07 EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTTS-......GS--.-SEEEE--- CS DNA_methylase 3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigDitkidkk......klpediDlLvgGfP 70 + dL +G+G +++g ++ g ++ +id +a +++++n ++ ++ +i+ i+ + k+p+ +D ++ +P tr|H9GNU1|H9GNU1_ANOCA 55 VADLGCGCGVLSIGSSMLGAGLCVGFDIDLDALDVFSKNAEEFELTNIDMIQCNvcslpdKMPKIFDTVIMNPP 128 579**************************************999999999998888777777754787776665 PP == domain 2 score: -2.3 bits; conditional E-value: 0.71 HHHHHHHHHHHHHTEE CS DNA_methylase 121 ktlkvilekleelGYe 136 +++kv +e l+el Y+ tr|H9GNU1|H9GNU1_ANOCA 170 EEWKVKMEVLAELRYD 185 4444444444444443 PP >> tr|G1KQQ9|G1KQQ9_ANOCA BCL2 interacting protein 1 OS=Anolis carolinensis OX=28377 GN=BNIP1 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.6 2.0 1.1e-05 0.033 169 291 .. 49 203 .. 17 209 .. 0.70 Alignments for each domain: == domain 1 score: 13.6 bits; conditional E-value: 1.1e-05 -------SS---GGG.....TSGGGTTS-EE...BTTTB--GGGSSSTT-EE--.......S---H....HHTS--........... CS DNA_methylase 169 vlvkvkefrfpkkkdleasktlrdlleekse...ldeektalsdklvekeekikkttkaseegypk....elsrnr........... 237 v +k + r+ +++ le+ +d ++ e l +e ++++++++++++ ++k++ a++ ++++ e tr|G1KQQ9|G1KQQ9_ANOCA 49 VKEKFHHLRLRIQE-LEQMAKEQDKES---EkqvLLQEVENHKKQMLSNQAAWRKANLACKIAIDNaekdE----Llrggdplrqrk 127 33333333333333.333333344444...1455999************************9999744442....344556666667 PP ..........B--TTS...-B----S-STT-..-B-TTS---EEEETTEEE--T...........TTGGG--B-BH CS DNA_methylase 238 ..........idkveelkglsatrrksgrge..klekelaeagklqknkerfkp..........viekkriRrLtp 291 + +e+l g+s+++ ++ r+ ++++ ++ + + ++ +e+fk+ +i+k++ R+Lt tr|G1KQQ9|G1KQQ9_ANOCA 128 ttkeslaegaSNITESLMGISRMMSQQVRQSeeTMQTLVNSSRTIVDANEEFKSmsgtiqlgrkLITKYNRRELTD 203 777777777745555555555555544443366999999999999999999999*999999999999999999997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (335 nodes) Target sequences: 18528 (9796552 residues searched) Passed MSV filter: 1723 (0.0929944); expected 370.6 (0.02) Passed bias filter: 595 (0.0321136); expected 370.6 (0.02) Passed Vit filter: 64 (0.00345423); expected 18.5 (0.001) Passed Fwd filter: 7 (0.000377807); expected 0.2 (1e-05) Initial search space (Z): 18528 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 0.32u 0.01s 00:00:00.33 Elapsed: 00:00:00.10 # Mc/sec: 32818.45 // [ok]