# 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/TRM.hmm.txt # target sequence database: proteomes/Tetrahymena_thermophila.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TRM [M=376] Accession: PF02005.15 Description: N2,N2-dimethylguanosine tRNA methyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-100 335.8 0.5 7.6e-100 335.3 0.5 1.1 1 tr|Q22HL7|Q22HL7_TETTS tRNA (guanine(26)-N(2))-dimethyltrans 2.6e-55 188.7 5.2 3.8e-55 188.2 5.2 1.2 1 tr|W7X4C4|W7X4C4_TETTS tRNA (guanine(26)-N(2))-dimethyltrans 0.0027 17.5 0.0 0.0058 16.4 0.0 1.5 1 tr|W7XD08|W7XD08_TETTS tRNA (guanine(37)-N1)-methyltransfera Domain annotation for each sequence (and alignments): >> tr|Q22HL7|Q22HL7_TETTS tRNA (guanine(26)-N(2))-dimethyltransferase OS=Tetrahymena thermophila (strain SB210) OX=3120 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 335.3 0.5 8.5e-104 7.6e-100 18 376 .] 108 505 .. 92 505 .. 0.91 Alignments for each domain: == domain 1 score: 335.3 bits; conditional E-value: 8.5e-104 --SS--GGGHHHHHHHHHH....HHHHHHHH-S-...EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT-- CS TRM 18 eeVFYNPvqefnRDlsvlvir.qlellkkklgek...ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneve 100 +eVFYNPvq fnRDl+vlvi+ + e+lk+ +ek i++ldaLsasGlRaiRf++E++ k+v+aNDise +l+ N+ ln+ + tr|Q22HL7|Q22HL7_TETTS 108 SEVFYNPVQVFNRDLTVLVIHmFKEYLKETRKEKfdgITILDALSASGLRAIRFSKELKDIKKVYANDISEASHKLMMDNFILNNLD 194 58******************966677766666668889************************************************9 PP .GGEEEE-S-HHHHHC.........--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHHSSB--- CS TRM 101 .eivvineddAnvlla.........ekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrkYgavalk 177 +++ +dA l++ ++ rfdviDlDP+G+ apfld a+q + + lL++T+TD+ L+G ++kc+ Yg++ k tr|Q22HL7|Q22HL7_TETTS 195 lSKIEMTLKDAVQLMYeqkfrsssgDRNARFDVIDLDPYGTCAPFLDCAIQGAVGETLLCITSTDSRILCGPDTQKCYYLYGSSRAK 281 7689************9999988888899********************************************************** PP STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT...............--EE CS TRM 178 selcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgC...............lsee 249 ++ E a+Ri+l++ ++ a++Y k+++pll+++++fYvrvf+ +k g+ + ++l ++g v+hC +C tr|Q22HL7|Q22HL7_TETTS 282 IAAYEENAVRIILYTANNIANRYGKFITPLLCYMSEFYVRVFLIIKPGKLECGRSLVRTGNVFHCDNCqnqyfqtfgkqskakQ--- 365 ********************************************************************7777666655433320... PP EE--GGG--..............SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT.....-TTS-HHHHHHHHHHHHHH.... CS TRM 250 kvkglakfk..............aecehcgaklhlaGPlwlgplkdkefveevleeaekek...eeelkkrvkklLklikeEl.... 315 + + c++cg+++ + GP+w ++l+d+ef+++ ++ ++++k + ++kk+++++L+ i+ E tr|Q22HL7|Q22HL7_TETTS 366 --------SdaqkhvpqklnlpsNICNQCGESFTINGPIWTDKLNDQEFIQKTIDYLNSDKfdlPLATKKKIEGMLHSIQLEQkagv 444 ........13334456667788799******************************9999877666777***********99864443 PP S--SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHHH CS TRM 316 ldaplyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevlr 376 + pl ++ ++l++++k++vp++kk+ sa+k+l++ + +t ++p kTnap e v +v+r tr|Q22HL7|Q22HL7_TETTS 445 DNIPLGFNFEHLSKMMKTTVPSKKKIFSAIKSLNYSIEQTYLNPAIYKTNAPSEIVFDVIR 505 5789******************************************************986 PP >> tr|W7X4C4|W7X4C4_TETTS tRNA (guanine(26)-N(2))-dimethyltransferase OS=Tetrahymena thermophila (strain SB210) OX=3120 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 188.2 5.2 4.2e-59 3.8e-55 14 376 .] 101 521 .. 83 521 .. 0.80 Alignments for each domain: == domain 1 score: 188.2 bits; conditional E-value: 4.2e-59 --TT--SS--GGGHHHHHHHHHH....HHHHHHHH-S-...EEEEESS-TTSHHHHHHHHH-S-E..E..EEEEE-S-HHHHHHHHH CS TRM 14 vskkeeVFYNPvqefnRDlsvlvir.qlellkkklgek...ikvldaLsasGlRaiRfalEvpgv..k..evlaNDisekAvelike 92 +++ + FYN vq + RD+++lv + +++ l+ g+ ++l++ ++sG++a+R+a+E++ + +v+ Di+ e k tr|W7X4C4|W7X4C4_TETTS 101 KENHFKMFYNLVQLVERDITLLVANqYFKDLEITNGQSfkgARILQGKASSGVKALRYAKEIDPSyiQdiTVIEKDINFP--EYFKL 185 3455689***************985566555555555533378******************9864223225666777643..45555 PP HHHHTT--.GGEEEE-S-HHHHHC..........--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHH CS TRM 93 Nvklneve.eivvineddAnvlla..........ekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekcl 168 +++n+++ +i +++ n + + + +d+iD++ +Gs+ + + +a++ vk++g+++ TD+++L+G kc+ tr|W7X4C4|W7X4C4_TETTS 186 LAHYNDIDmSKFKIVNKETNHFYLskilenmdkyDQPELYDFIDIEEYGSSIDTIRQAIKLVKNGGMISAMFTDMSTLCGPNVIKCY 272 567888886344544445555433366666666667788************************************************ PP HHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT.......... CS TRM 169 rkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgC.......... 245 + Y+ + ++ + E a+Ri+ +++ a++ + +ep++s+++dfY+++f++v+++ ++++k lekl lv++Cs+C tr|W7X4C4|W7X4C4_TETTS 273 SSYNKFRIRLASLNENAIRIIYSTILDIATQNNYSIEPVVSFQSDFYIKIFFRVHHNGVESQKALEKLSLVYQCSECpnyhvhtiak 359 *****************************************************************************8888887666 PP ....--EEEE--GGG--....................SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS........ CS TRM 246 ....lseekvkglakfk....................aecehcgaklhlaGPlwlgplkdkefveevleeaekekeeel........ 300 + e++ + +c+ c+++ l GPlw +pl++ +fv++vl++++++ +e++ tr|W7X4C4|W7X4C4_TETTS 360 vqqnTIENV-------QngtlklessmdlklnelkvpSNCNVCESSWILNGPLWNQPLHNYKFVQNVLRNLQSTGSEKVfsknkiml 439 554422233.......244444558888889999999**********************************9987444445444456 PP ...-HHHHHHHHHHHHHH..S--SS-EEHHHHHHHHT-SS.---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHHH CS TRM 301 ...kkrvkklLklikeEl..ldaplyydlsqlasvlklsv.pplkkvvsalkelgfevsrtHakpkaikTnapleavvevlr 376 + ++ + L++i +E + l y+l + k ++ p ++++ +al ++g+ + r+ +++k kTnap +++ + +r tr|W7X4C4|W7X4C4_TETTS 440 iqsHLKLTAYLEAILQEKefDKFILGYNLTLINGFYKAKTyPTTNHIKRALARAGYTINRSIFEKKIYKTNAPSNVIFDTMR 521 65555677889999988763445678*********99987266789999******************************997 PP >> tr|W7XD08|W7XD08_TETTS tRNA (guanine(37)-N1)-methyltransferase OS=Tetrahymena thermophila (strain SB210) OX=312017 G # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.4 0.0 6.4e-07 0.0058 21 115 .. 205 286 .. 179 306 .. 0.71 Alignments for each domain: == domain 1 score: 16.4 bits; conditional E-value: 6.4e-07 S--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--G.GEEEE CS TRM 21 FYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklnevee.ivvin 106 ++ + ++ RD ++ + ++ + +vld + + G aiR a+ +v+ ND++++ ++ + N + n+ve+ ++ +n tr|W7XD08|W7XD08_TETTS 205 YFCSRLQTERDRVLKL----------IKPNETVLDLFCGVGPLAIRAAKM---GCKVICNDLNPHCYDYLLINREKNNVEDkTLCFN 278 4445555555533333..........2222479***************97...567888*********************9466666 PP -S-HHHHHC CS TRM 107 eddAnvlla 115 + dA+ ++ tr|W7XD08|W7XD08_TETTS 279 N-DARKVVD 286 6.9998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (376 nodes) Target sequences: 26971 (16912921 residues searched) Passed MSV filter: 2330 (0.0863891); expected 539.4 (0.02) Passed bias filter: 416 (0.015424); expected 539.4 (0.02) Passed Vit filter: 35 (0.00129769); expected 27.0 (0.001) Passed Fwd filter: 3 (0.000111231); expected 0.3 (1e-05) Initial search space (Z): 26971 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.40u 0.01s 00:00:00.41 Elapsed: 00:00:00.13 # Mc/sec: 48917.37 // [ok]