# 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/Thermococcus_kodakarensis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-117 389.5 0.0 2.5e-117 389.3 0.0 1.0 1 sp|Q5JIB3|TRM1_THEKO tRNA (guanine(26)-N(2))-dimethyltrans 2.7e-08 30.5 0.0 3.6e-08 30.0 0.0 1.2 1 tr|Q5JJ78|Q5JJ78_THEKO Probable tRNA/rRNA methyltransferase 0.00022 17.6 0.0 0.0003 17.2 0.0 1.2 1 tr|Q5JD70|Q5JD70_THEKO Met-10+ like protein OS=Thermococcus 0.0066 12.7 0.0 0.0094 12.2 0.0 1.2 1 tr|Q5JIX8|Q5JIX8_THEKO N5-glutamine methyltransferase, HemK Domain annotation for each sequence (and alignments): >> sp|Q5JIB3|TRM1_THEKO tRNA (guanine(26)-N(2))-dimethyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 389.3 0.0 4.4e-120 2.5e-117 2 376 .] 10 374 .. 9 374 .. 0.95 Alignments for each domain: == domain 1 score: 389.3 bits; conditional E-value: 4.4e-120 TEEEEE----SS--TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHH CS TRM 2 eakikvedkevtvskkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAveli 90 a+i v+++ +++ ++VFYNPv+ nRD+svl+ +++l+ k +vldaLsa+G+R+iR+alE + ++ev++NDise+A+ l+ sp|Q5JIB3|TRM1_THEKO 10 LARILVPKA-ERIYD-APVFYNPVMSLNRDISVLA---VKVLGPK-----RVLDALSATGIRGIRYALE-TPAEEVWLNDISEEAYGLM 87 567788887.44444.7******************...8899999.....8******************.7899*************** PP HHHHHHTT--..............GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHH CS TRM 91 keNvklneve..............eivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspe 165 k+N++ln ++vvin++dAn l+ae+ ++fd++DlDPfGsp++fld+a++sv+++g+L+vTaTDt vL+Ga+ + sp|Q5JIB3|TRM1_THEKO 88 KKNASLNIDGelyeegdrsylwgeKLVVINKGDANRLMAENFRYFDFLDLDPFGSPVEFLDTALRSVRRNGVLAVTATDTGVLCGAYRN 176 ***9998555677889999***966**************************************************************** PP HHHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT--EEEE--G CS TRM 166 kclrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgClseekvkgl 254 +clrkY a +++ lcHE +lRil+++v+r+aakY+ ve+ll++ +d+Y+r+f+k+k+ga+k++k+l++lg++ ++g+ sp|Q5JIB3|TRM1_THEKO 177 ACLRKYLAEPIRGPLCHEAGLRILIGTVVRYAAKYDLGVEVLLAYHRDHYFRAFLKLKSGAKKADKSLSQLGFLWA--------DKSGR 257 **************************************************************************99........68899 PP GG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-EEHHHHHHHHT-SS---HHHHH CS TRM 255 akfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldaplyydlsqlasvlklsvpplkkvvs 343 +++ ++ ++ k + GPlwlgplkd+ fvee+le a++ + +k+++ +L+li+eE ld+p+ yd++ la+ +l+ p+l+ +++ sp|Q5JIB3|TRM1_THEKO 258 FEY--RRGFLPDKPGASGPLWLGPLKDESFVEELLESARD--HPLAHKKTLSFLQLISEE-LDVPFHYDTHTLARACSLTPPKLDVIIQ 341 995..899*******************************9..4566999***********.**************************** PP HH....TT-EE-TTSTTEEE-SS-HHHHHHHHH CS TRM 344 alkelgfevsrtHakpkaikTnapleavvevlr 376 l+elg+ +++tH++p+++kT+ap+ +v ev++ sp|Q5JIB3|TRM1_THEKO 342 RLRELGHSATKTHFSPTSVKTDAPFGVVAEVMK 374 *******************************96 PP >> tr|Q5JJ78|Q5JJ78_THEKO Probable tRNA/rRNA methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 30.0 0.0 6.3e-11 3.6e-08 50 128 .. 212 297 .. 119 301 .. 0.86 Alignments for each domain: == domain 1 score: 30.0 bits; conditional E-value: 6.3e-11 -......EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC...--SS-EEEEEE- CS TRM 50 k......ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvlla...ekkkrfdviDlD 127 + ++vld ++ +G ai a+ g+ ev+a D s+ A++++keN+kln ve+ ++ + A +++ ++ ++fd++ lD tr|Q5JJ78|Q5JJ78_THEKO 212 EkyvkpgMRVLDVFTYTGGFAIHAAVA--GADEVVAVDKSPWAINMVKENAKLNGVEDKMKYIVGSAFPVMEemiKRGEKFDIVILD 296 145555599*********99*999965..*****************************9999999*****998888999******** PP - CS TRM 128 P 128 P tr|Q5JJ78|Q5JJ78_THEKO 297 P 297 9 PP >> tr|Q5JD70|Q5JD70_THEKO Met-10+ like protein OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) OX # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.2 0.0 5.1e-07 0.0003 52 149 .. 184 275 .. 133 277 .. 0.80 Alignments for each domain: == domain 1 score: 17.2 bits; conditional E-value: 5.1e-07 EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHH CS TRM 52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspapflds 138 v+d +++ G +i a+ +k v+a Di++ Av ++eN kln+ + v + +d + + ++k ++ l f + fl tr|Q5JD70|Q5JD70_THEKO 184 IVFDMFAGVGPYSILLAKK---AKLVFACDINPWAVRYLEENKKLNKTPN-VIPILGDVRKVAGQIKADRVIMNLPKF--ADRFLKE 264 5889999999999988877...899*************************.555566999999888888888888888..6789999 PP HHHHEEEEEEE CS TRM 139 avqsvkekglL 149 a+ svk++g++ tr|Q5JD70|Q5JD70_THEKO 265 AMMSVKSGGIV 275 99999999986 PP >> tr|Q5JIX8|Q5JIX8_THEKO N5-glutamine methyltransferase, HemK family OS=Thermococcus kodakarensis (strain ATCC BAA-918 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 12.2 0.0 1.6e-05 0.0094 58 126 .. 43 104 .. 25 126 .. 0.79 Alignments for each domain: == domain 1 score: 12.2 bits; conditional E-value: 1.6e-05 -TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE CS TRM 58 sasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDl 126 +++G+ a+ a ++ vl Di++ Avel +eN+++n + + v+++ + l+++++ +fdvi tr|Q5JIX8|Q5JIX8_THEKO 43 TGTGIIALLLARK---ARWVLGVDINPLAVELARENARINGIIN-VEFRLS---DLFENVSGEFDVITF 104 5667666666655...7889999********************9.889884...477788899999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (376 nodes) Target sequences: 2301 (637680 residues searched) Passed MSV filter: 95 (0.0412864); expected 46.0 (0.02) Passed bias filter: 86 (0.0373751); expected 46.0 (0.02) Passed Vit filter: 14 (0.00608431); expected 2.3 (0.001) Passed Fwd filter: 4 (0.00173837); expected 0.0 (1e-05) Initial search space (Z): 2301 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 23976.77 // [ok]