# 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/TruD.hmm.txt # target sequence database: proteomes/Ciona_intestinalis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TruD [M=416] Accession: PF01142.17 Description: tRNA pseudouridine synthase D (TruD) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-65 219.5 0.1 1.4e-59 201.9 0.0 2.4 2 tr|F6PJM3|F6PJM3_CIOIN Uncharacterized protein OS=Ciona inte 8e-49 166.5 0.0 1.1e-48 166.0 0.0 1.2 1 tr|F6SVP7|F6SVP7_CIOIN Uncharacterized protein OS=Ciona inte ------ inclusion threshold ------ 0.082 11.6 0.0 4.5 5.9 0.0 2.0 2 tr|F6WVN8|F6WVN8_CIOIN Uncharacterized protein OS=Ciona inte Domain annotation for each sequence (and alignments): >> tr|F6PJM3|F6PJM3_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 GN=LOC100181071 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 15.1 0.1 1.2e-06 0.0069 2 32 .. 9 39 .. 8 56 .. 0.86 2 ! 201.9 0.0 2.6e-63 1.4e-59 39 416 .] 153 545 .. 133 545 .. 0.90 Alignments for each domain: == domain 1 score: 15.1 bits; conditional E-value: 1.2e-06 TruD 2 lgielyvtdtegigGrlrespeDFiVeEiee 32 +g+ y+ +++g+ G l+ +++DF+V+Ei tr|F6PJM3|F6PJM3_CIOIN 9 VGMTEYIGKHKGFTGILKMRYQDFMVNEIDL 39 89***************************43 PP == domain 2 score: 201.9 bits; conditional E-value: 2.6e-63 TruD 39 akegeylvlrvekrnwdtldlvrelaralgisrkr.vgfaGtKDkrAvTtQlisirkvepeelekl.ei.kdvelevvgrarrklrl 122 + +y+ + + k+n+ t+d+v+ + ++l++ + r +++aG KDkr+vT+Q ++ ++pe+l + +i +++++ ++++ + + rl tr|F6PJM3|F6PJM3_CIOIN 153 DRGFPYCKFVLYKENIATMDAVNLILKKLNLRHARcFQYAGNKDKRGVTVQEVTT-SISPERLVPVnQIlSNIRVGNLVSCKTAKRL 238 3334789999*********************9988579**************995.46666654443444***************** PP TruD 123 GdLaGNkFeirvrdvaeeeeaakraeeileelkekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAveayvgkpfeeesedtre 209 GdL GN+F i++r++ + e ++++++ +++ +++g + NyfG+QRFG++ t+++Gk i+ +ee v+ +++ f++ se+t + tr|F6PJM3|F6PJM3_CIOIN 239 GDLNGNQFSIVIRNTLDIE--ESDLKAAIKSFSQTG-FINYFGMQRFGTNNVPTYEIGKSIISSRWEETVDLILSSCFKDCSEETIN 322 **************85555..489**********99.************************************************** PP TruD 210 areavaetgdleealeelpkslryEramlkrLae.kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvv 295 ++ e++++++a ++l+++ ++E +l + + pk+ ++l+++p+n ++l++h+yqS+++Nr++s+R+ d+pv GD+v tr|F6PJM3|F6PJM3_CIOIN 323 LIRNWREENNAKKAFDKLNRRSSFEGYLLLGISHfGPKQLVQSLARIPRNTRMLYLHSYQSFVWNRIVSRRFLTF--GDSPVVGDLV 407 ********************************9999************************************988..589******* PP TruD 296 ifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRail 382 + +e+ ++e+n+++++ v++pl+G +++ + + + ++ ++ +g+e ++F+ k++e G++R+i+ tr|F6PJM3|F6PJM3_CIOIN 408 LAGNEK------EVYMHEENIDNYS------IHDVIMPLPGHKVTYPTNSALQWYKDEFKAAGIEESMFDH-KVKEYYLPGAYRKII 481 *99887......8888999999988......44799**********************************5.579************ PP TruD 383 lrve..............................dlelsaeedeltleFsLpkGsYATvvlrEi 416 +++ + e + + + l ++FsL + +YATv +rE+ tr|F6PJM3|F6PJM3_CIOIN 482 NKPNdvewdivkyndyqkpllasdkdilqggerpSGEKDGKFTALRISFSLSSSCYATVAMREV 545 ***99**********************999865522333333459******************6 PP >> tr|F6SVP7|F6SVP7_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 GN=LOC100184413 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 166.0 0.0 2e-52 1.1e-48 56 416 .] 1 416 [. 1 416 [. 0.81 Alignments for each domain: == domain 1 score: 166.0 bits; conditional E-value: 2e-52 TruD 56 tldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl.......ei..kdvelevvgrarrklrlGdLaGNkFeir 133 t++++++l+ l ++++++++aG+KDkrA+T Q +++++v++++ +++ ++ ++++++ v+ ++ +l +G+L+GN+F+i+ tr|F6SVP7|F6SVP7_CIOIN 1 TIQAIHQLSLLLDVKSSEFSYAGMKDKRAITLQRVAVSGVSKDNFKNVykllevsHVlpDHLRISHVIVTSLRLITGNLVGNRFDIK 87 67899***************************************999998887663367899************************* PP TruD 134 vrdv.aeeeeaakraeeileelkekg.....gvPNyfGvQRFGsrrpvthl...........vGkaivkgdleeAveayvgkpfeee 203 +r+v + + + +++ i+ + + g+ NyfG QRFG+ r t++ vG a++k+++++Ave+++ + e+ tr|F6SVP7|F6SVP7_CIOIN 88 LRNVhGGKTTINIHLTLITTIIYAILffktkGFINYFGPQRFGR-RIDTKEpgsipqweapsVGLAMLKQNMKRAVEILLLPAVEAG 173 ***95544444444444444333322555568***********9.67776444444444444*****************98887766 PP TruD 204 s..edtreareavaetgdleealeelpkslryEramlkrLae...kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglp 285 + +d ++ + ++++t ++eeal+++p++ E +l++L++ +++ +kAl ++p + + ++ h+y Syl+Nrv seRl++ tr|F6SVP7|F6SVP7_CIOIN 174 KpiDDEQKGKLLFQQTWNVEEALKLMPRHRFREIGILQSLQQtssSEQFCSKALLTIPFKERTFYAHSYSSYLWNRVASERLRQL-G 259 5236888999999****************999**********776666699********************************87.3 PP TruD 286 ldepveGDvvifaeer.lpdtdrlqlvteknveevkrliergraf.vtaplvGtetelaegevgeierevleeegl.......eled 363 +++eGD+vi+++ + +++ + v+ ++vk ++r+ + v++pl+G +++ + +++ +++++e++l + tr|F6SVP7|F6SVP7_CIOIN 260 -CDVIEGDLVIQRTGDsENIERHDSEVHVVVSDDVK--CNRFSIYdVVLPLPGNRVQYPPN-LDAVYDRIFKEDQLfigtepkASNY 342 .58*********977732233333445555555555..7888764489**********765.6889999**9999855554433456 PP TruD 364 FklpklpelsskGtrRaillrve......................dlelsaeedeltleFsLpkGsYATvvlrEi 416 F+++k +l+ Gt+R+++ +++ ++l +++ +l l+F Lp+ +YAT++lrE+ tr|F6SVP7|F6SVP7_CIOIN 343 FRVNK-LKLNLCGTYRRLIEKPKnftinwesdvssqavtgdegmrCTTLADDGATLGLKFDLPSSCYATSILREL 416 88998.89**************9*****************99665334445555699****************96 PP >> tr|F6WVN8|F6WVN8_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 3.9 0.1 0.0033 18 351 392 .. 9 45 .. 2 53 .. 0.72 2 ? 5.9 0.0 0.00082 4.5 288 368 .. 59 135 .. 51 141 .. 0.82 Alignments for each domain: == domain 1 score: 3.9 bits; conditional E-value: 0.0033 TruD 351 revleeegleledFklpklpelsskGtrRaillrvedlelsa 392 + e l+++d k + ++ ++s+G +R++ ++++++ +++ tr|F6WVN8|F6WVN8_CIOIN 9 N-----EALTADDLKSQMFQSMKSAGVVRQLKVQLRQTMINE 45 3.....44555566655555899**********999766554 PP == domain 2 score: 5.9 bits; conditional E-value: 0.00082 TruD 288 epveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpk 368 + + D++ + + +++ + v+++ ++ v ++i++ + t+ l+ e+ ++ + +++++l++ gl+ +d ++ + tr|F6WVN8|F6WVN8_CIOIN 59 NLENSDLIAATMH---RRKSYSWVQTALDNIVLHHIKQSKYYYTLSLFEQESSVS-CYSKSLTEQLLSRLGLHDSDIEIDS 135 5555666666644...48889999999999*********************9995.66899999*********99988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (416 nodes) Target sequences: 16678 (5370518 residues searched) Passed MSV filter: 570 (0.0341768); expected 333.6 (0.02) Passed bias filter: 267 (0.0160091); expected 333.6 (0.02) Passed Vit filter: 22 (0.0013191); expected 16.7 (0.001) Passed Fwd filter: 3 (0.000179878); expected 0.2 (1e-05) Initial search space (Z): 16678 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.18u 0.01s 00:00:00.19 Elapsed: 00:00:00.06 # Mc/sec: 37235.59 // [ok]