# 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/Natronomonas_moolapensis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-48 160.8 0.0 9.6e-48 160.5 0.0 1.0 1 tr|M1XQI7|M1XQI7_NATM8 Site-specific DNA-methyltransferase ( 9e-42 140.9 0.0 1e-41 140.7 0.0 1.0 1 tr|M1Y1K5|M1Y1K5_NATM8 Site-specific DNA-methyltransferase ( 0.0037 14.0 0.0 0.0047 13.6 0.0 1.1 1 tr|M1XN99|M1XN99_NATM8 tRNA(Phe) (4-demethylwyosine(37)-C(7) Domain annotation for each sequence (and alignments): >> tr|M1XQI7|M1XQI7_NATM8 Site-specific DNA-methyltransferase (Cytosine-specific) OS=Natronomonas moolapensis (strain D # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 160.5 0.0 1.1e-50 9.6e-48 2 333 .. 4 352 .. 3 354 .. 0.78 Alignments for each domain: == domain 1 score: 160.5 bits; conditional E-value: 1.1e-50 EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-..-SEEEES-TTTS-......GS--...-SEEEE---GGGTECTSE CS DNA_methylase 2 kfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk.kvsigDitkidkk......klpe..diDlLvgGfPCqpfSvaGk 79 + +dLf+G GG+++gle+ag+++ + +++d++++ Ye+n+ + + D++ ++++ +p d D+L ++ PCqp+S G+ tr|M1XQI7|M1XQI7_NATM8 4 TAVDLFCGSGGLSHGLEQAGISVNVGVDKDPHCKHAYEQNIDaEYRQTDVRPLSQDpervarMFPWdsDLDVLGACAPCQPYSTMGQ 90 679************************************************99999999**98887545*****************9 PP E--TTSGGG...HHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEE...EEEEEGGGTT-SB--EEEEEEE CS DNA_methylase 80 qkgfedtrg...tLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYevs...ykllnasdyGvpQnReRvfivg 160 +k ++ L+ +i +i + +P++++ ENV+++ k d + ++++++l++lGY+v+ k + + +yG+pQnR+R+++++ tr|M1XQI7|M1XQI7_NATM8 91 SKNKTHQDHqkwGLLKDIKKISEYVEPDIIITENVPQVRKDD---VYDEFVQTLKDLGYHVNddeNKKVYCPEYGIPQNRKRWVMMA 174 5554444434479************************99985...69999***********999989999***************** PP EEGGG----------SS---GGG.....TSGGGTTS-EEBTTTB--GGGS.SSTT-EE--.......S---H.......HHTS--B- CS DNA_methylase 161 irkdlelnvlvkvkefrfpkkkdleasktlrdlleekseldeektalsdk.lvekeekikkttkaseegypk.......elsrnrid 239 +++ ++++ ++ e++++ + +++++ l++ + + ++ l ++ +++++ + ++ +++++++ l ++++ tr|M1XQI7|M1XQI7_NATM8 175 SKEGP-ISLPDPLYENESEYPT---VREAIGHLPPLQAGEVHPEYDLHQArSLSEKNLERIRNMKPGGDWRLweedgltHLLADCHK 257 *9985.4556666666666664...56666666665544444444443330334444444456666666664444666655555577 PP -TTS...-B----S-STT--B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBH.....HHHHHHHTS- CS DNA_methylase 240 kveelkglsatrrksgrgeklekelaeagklqknkerfkpviekkriRrLtprEaarlqGfPddfefgskks.....aaykqiGnsV 321 k+ ++ +++r + k+ + ++++ ++ ++ f ++ + R+L+ E a lq+fP+d++f + + + ++iGn+V tr|M1XQI7|M1XQI7_NATM8 258 KSSGRSYKAPYSRMEPD--KVAPTITTQFYNYGSGR-FG-HYDTDQDRALSLLEGALLQTFPEDYDFYDEWEevgvkNLGRLIGNAV 340 77776666666666664..44444444444433333.44.4899************************999989999999******* PP -HHHHHHHHHHH CS DNA_methylase 322 pvpvieaiakei 333 p+ + ++i++ i tr|M1XQI7|M1XQI7_NATM8 341 PPLLGKHIGRGI 352 ********9876 PP >> tr|M1Y1K5|M1Y1K5_NATM8 Site-specific DNA-methyltransferase (Cytosine-specific) OS=Natronomonas moolapensis (strain D # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 140.7 0.0 1.1e-44 1e-41 2 333 .. 4 347 .. 3 349 .. 0.79 Alignments for each domain: == domain 1 score: 140.7 bits; conditional E-value: 1.1e-44 EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-..-SEEEES-TTTS-.........GS--.-SEEEE---GGGTECTS CS DNA_methylase 2 kfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk.kvsigDitkidkk.........klpediDlLvgGfPCqpfSvaG 78 + idLf+G+GG++ gle+ag+ + a ++id++ Ye+n+ + ++Di +++ + + ++d lL g+ PCqpfS tr|M1Y1K5|M1Y1K5_NATM8 4 SAIDLFCGAGGLTNGLERAGICVEAGIDIDPDSEFPYEQNNDaEFLLKDIAELAREepemvteyfDSEADATLLAGCAPCQPFSPLT 90 679***************************************************999*999974433335789***********988 PP EE--TTSGGG.HHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEE...EEEEEGGGTT-SB--EEEEEEEE CS DNA_methylase 79 kqkgfedtrg.tLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYevs...ykllnasdyGvpQnReRvfivgi 161 + ++ + ++ ++ + +i++e +P+++++ENV ++ + d + +++++ l++lGY+++ + + + +y++pQ R+R+++++ tr|M1Y1K5|M1Y1K5_NATM8 91 HGSDSSEHSKyGMLRAFLEIVRESDPDFVVMENVFEVRHAD---VYDEFIDGLDQLGYNLNpksDRRVYCPEYDIPQTRRRWVVLAS 174 7655555544579*********************9998885...69999************44434689****************** PP EGGG---.-------SS---GGG......TSGGGTTS-EEBTTTB--GGGSSSTT-EE--.......S---HHHTS--B--TTS... CS DNA_methylase 162 rkdleln.vlvkvkefrfpkkkd.leasktlrdlleekseldeektalsdklvekeekikkttkaseegypkelsrnridkveelkg 246 +k+++ + + + ++p+ kd + + l+ +++k d ta s + ++ ++ + + + s++++p e+ r k ++++ tr|M1Y1K5|M1Y1K5_NATM8 175 KKGRIDLgAPLNPEPADYPTVKDrIDHLDPLEAGETSK--EDPLHTARSLSETNIKRIRCSNPGGSWKDWP-EELRLDCHKKASGQT 258 **986557555555556666654233333333333333..3333444444444444444445688888888.777777777777788 PP -B----S-STT--B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBH.....HHHHHHHTS--HHHHHH CS DNA_methylase 247 lsatrrksgrgeklekelaeagklqknkerfkpviekkriRrLtprEaarlqGfPddfefgskks.....aaykqiGnsVpvpviea 328 + a + + +e+ + +++ ++l++ ++ + R+L+ rE a +q+fP+d+ f+ + + ++ ++iGn+Vp+ + e tr|M1Y1K5|M1Y1K5_NATM8 259 YEAVYGRMVADEPAPTITTQFYNLGSGRFG---HYDTDQDRALSLREGAMIQTFPEDYRFADDLEeveiiKVGRLIGNAVPPRLGEV 342 888888888878888888888888777775...4899*************************999898999999**********999 PP HHHHH CS DNA_methylase 329 iakei 333 +++++ tr|M1Y1K5|M1Y1K5_NATM8 343 VGDRV 347 98876 PP >> tr|M1XN99|M1XN99_NATM8 tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase OS=Natronomonas moolapen # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 13.6 0.0 5.2e-06 0.0047 2 42 .. 198 237 .. 197 261 .. 0.83 Alignments for each domain: == domain 1 score: 13.6 bits; conditional E-value: 5.2e-06 EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH- CS DNA_methylase 2 kfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanf 42 +++d+faGiG f+l +++a+ v a+eid++a + n tr|M1XN99|M1XN99_NATM8 198 RVFDMFAGIGYFSLPMARAE-ASVTAAEIDPTAHRRLVENA 237 689*****************.889999****9987666665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (335 nodes) Target sequences: 2723 (809592 residues searched) Passed MSV filter: 68 (0.0249725); expected 54.5 (0.02) Passed bias filter: 57 (0.0209328); expected 54.5 (0.02) Passed Vit filter: 8 (0.00293794); expected 2.7 (0.001) Passed Fwd filter: 3 (0.00110173); expected 0.0 (1e-05) Initial search space (Z): 2723 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 13560.67 // [ok]