# 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/Petromyzon_marinus.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-54 183.5 0.0 1e-47 162.5 0.0 2.9 2 tr|S4RNV6|S4RNV6_PETMA Pseudouridylate synthase 7, like OS=P Domain annotation for each sequence (and alignments): >> tr|S4RNV6|S4RNV6_PETMA Pseudouridylate synthase 7, like OS=Petromyzon marinus OX=7757 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.2 0.0 9.8e-08 0.0013 5 38 .. 15 48 .. 12 58 .. 0.82 2 ! 162.5 0.0 7.5e-52 1e-47 39 415 .. 317 722 .. 304 723 .. 0.85 Alignments for each domain: == domain 1 score: 17.2 bits; conditional E-value: 9.8e-08 TruD 5 elyvtdtegigGrlrespeDFiVeEieefsgeee 38 +y+ ++g+ G +++speDFiV Ei e s++++ tr|S4RNV6|S4RNV6_PETMA 15 YYYIGRHPGFCGAIKQSPEDFIVVEIDEHSNRAD 48 58999*********************77665433 PP == domain 2 score: 162.5 bits; conditional E-value: 7.5e-52 TruD 39 akegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelekl....eikdvelevvgrarrklr 121 + g y+v++++k+n++tl +++ la++lg+ +++++aGtKDk+AvT Q + ++kv+p++l+++ + +++++ + ra r+lr tr|S4RNV6|S4RNV6_PETMA 317 IDGGIYTVFTLQKTNMETLGAISMLASELGVLPSDFSYAGTKDKKAVTFQRMVVQKVTPSRLQEAaarlQARGLRVAAAKRAARPLR 403 57799********************************************************9988776688**************** PP TruD 122 lGdLaGNkFeirvrdv.aeee.......eaakraeeileelkekggvPNyfGvQRFGsrrpv.thlvGkaivkgdleeAveayvgkp 199 lG+L+GN+F++++r+v a + ++++e+ ++ + e+g + Ny+G QRFG+ +++ t ++Gk+++kg+l++A++ +++ tr|S4RNV6|S4RNV6_PETMA 404 LGELWGNHFRVTLRGVgAPTAtpqpddaAVRDCVERSVRGVVEHG-FINYYGPQRFGASQSIkTDEIGKHLLKGELDKALKLFFTPE 489 ***************965444566665544556666666666665.************9987489****************999866 PP TruD 200 feeesedtreareavaetgdleealeelpkslryEramlkrLae...kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerg 283 + ++ +++a++++ et ++++ ++l + r+ +k L ++ + ++++++ l v ++ ++ s ++e+ tr|S4RNV6|S4RNV6_PETMA 490 A--GDDAVNQAKRLFLETVNIKNQCDLLTTFGTRRRTAIKLLWAfsgLAEALPHCWHDVSSESCLLCVIVTVNIIYPEISSLKIESS 574 5..5567778999999**************9999999999999966566677777888****9*********************986 PP TruD 284 ...lpldepveGDvvifaeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklp 367 +++ + ve + ++ + ++++++vte++ ++ i+ +v++p++G++++ ++ e+g+ r+ l+++gl + F++ tr|S4RNV6|S4RNV6_PETMA 575 ggiVQWSQLVESSSSVVQS--ICLSSKVHVVTEEEEANEVYTID----QVVLPMPGSSVRYPDNEAGAAYRATLRRDGLADSAFRVA 655 2335677777776666664..45888889998866554444443....589**********************************99 PP TruD 368 klpelsskGtrRaillrve....................dlelsaeedeltleFsLpkGsYATvvlrE 415 + ++s G++R++l r++ ++ + ++++l+++F Lp+ +YATv l E tr|S4RNV6|S4RNV6_PETMA 656 E-LRVSLPGAYRRLLARPAnvslawterglpgattsgseETFAVGSSSSLVITFDLPSSCYATVCLGE 722 9.89**************99************99998853333334556***************9977 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (416 nodes) Target sequences: 13539 (5048892 residues searched) Passed MSV filter: 370 (0.0273285); expected 270.8 (0.02) Passed bias filter: 195 (0.0144028); expected 270.8 (0.02) Passed Vit filter: 17 (0.00125563); expected 13.5 (0.001) Passed Fwd filter: 1 (7.38607e-05); expected 0.1 (1e-05) Initial search space (Z): 13539 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.15u 0.01s 00:00:00.16 Elapsed: 00:00:00.05 # Mc/sec: 42006.78 // [ok]