Mercurial > repos > yufei-luo > s_mart
diff commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/OutputHmmpfamTest @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/OutputHmmpfamTest Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,406 @@ +hmmpfam - search one or more sequences against HMM database +HMMER 2.3.2 (Oct 2003) +Copyright (C) 1992-2003 HHMI/Washington University School of Medicine +Freely distributed under the GNU General Public License (GPL) +- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +HMM file: /home/choede/hmmer3/Pfam_fs +Sequence file: ConsensusTestFile_aaWithoutStop.fsa +- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +Query sequence: blumeria_Grouper_590_20:NoCat_1 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +DUF234 Archaea bacterial proteins of unknown 3.2 1.5 1 +DUF1414 Protein of unknown function (DUF1414) 2.9 6.3 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +DUF234 1/1 91 108 .. 5 22 .. 3.2 1.5 +DUF1414 1/1 111 119 .. 1 9 [. 2.9 6.3 + +Alignments of top-scoring domains: +DUF234: domain 1 of 1, from 91 to 108: score 3.2, E = 1.5 + *->VyPNrseIEsGnikevle<-* + VyPN++ IEs ++k++++ + blumeria_G 91 VYPNIEIIESSTPKPLIN 108 + +DUF1414: domain 1 of 1, from 111 to 119: score 2.9, E = 6.3 + *->HkAPvDLSL<-* + H ++DLSL + blumeria_G 111 HXSSPDLSL 119 + +// + +Query sequence: blumeria_Grouper_590_20:NoCat_2 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- + [no hits above thresholds] + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- + [no hits above thresholds] + +Alignments of top-scoring domains: + [no hits above thresholds] +// + +Query sequence: blumeria_Grouper_590_20:NoCat_3 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +CPW_WPC Plasmodium falciparum domain of unknown func 1.5 7.7 1 +HECT HECT-domain (ubiquitin-transferase) 0.0 9.2 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +CPW_WPC 1/1 30 37 .. 1 9 [. 1.5 7.7 +HECT 1/1 55 69 .. 341 355 .] 0.0 9.2 + +Alignments of top-scoring domains: +CPW_WPC: domain 1 of 1, from 30 to 37: score 1.5, E = 7.7 + *->CerdYsisk<-* + C++dYs sk + blumeria_G 30 CQFDYS-SK 37 + +HECT: domain 1 of 1, from 55 to 69: score 0.0, E = 9.2 + *->LllAIneeteGFgle<-* + Ll+A+n+ + G+ ++ + blumeria_G 55 LLTAVNNANTGYTQS 69 + +// + +Query sequence: blumeria_Grouper_590_20:NoCat_4 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +DUF46 Putative integral membrane protein DUF46 6.4 0.11 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +DUF46 1/1 82 91 .. 173 182 .] 6.4 0.11 + +Alignments of top-scoring domains: +DUF46: domain 1 of 1, from 82 to 91: score 6.4, E = 0.11 + *->YkLGlKdVpW<-* + Y+LGlK V++ + blumeria_G 82 YLLGLKGVWY 91 + +// + +Query sequence: blumeria_Grouper_590_20:NoCat_5 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +POC4 POC4 chaperone -1.7 6.3 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +POC4 1/1 121 125 .. 276 280 .] -1.7 6.3 + +Alignments of top-scoring domains: +POC4: domain 1 of 1, from 121 to 125: score -1.7, E = 6.3 + *->SGLYI<-* + SGLYI + blumeria_G 121 SGLYI 125 + +// + +Query sequence: blumeria_Grouper_590_20:NoCat_6 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- + [no hits above thresholds] + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- + [no hits above thresholds] + +Alignments of top-scoring domains: + [no hits above thresholds] +// + +Query sequence: blumeria_Grouper_4152_12:NoCat_1 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +Peptidase_S29 Hepatitis C virus NS3 protease 4.7 1.1 1 +DGOK 2-keto-3-deoxy-galactonokinase 0.5 1.3 1 +TNV_CP Satellite tobacco necrosis virus coat p 0.1 7.9 1 +TrbL TrbL/VirB6 plasmid conjugal transfer pr 0.8 8 1 +Amino_oxidase Flavin containing amine oxidoreductase -0.6 9.1 1 +DUF1301 Protein of unknown function (DUF1301) 0.4 9.9 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +Amino_oxidase 1/1 27 38 .. 471 482 .] -0.6 9.1 +TrbL 1/1 33 67 .. 231 285 .] 0.8 8 +TNV_CP 1/1 58 80 .. 167 189 .. 0.1 7.9 +DGOK 1/1 94 109 .. 283 298 .] 0.5 1.3 +Peptidase_S29 1/1 113 127 .. 1 15 [. 4.7 1.1 +DUF1301 1/1 148 157 .. 1 10 [. 0.4 9.9 + +Alignments of top-scoring domains: +Amino_oxidase: domain 1 of 1, from 27 to 38: score -0.6, E = 9.1 + CS HHHHHHHHHHHH + *->veSGlrAAaril<-* + veSG rAA +l + blumeria_G 27 VESGXRAASTLL 38 + +TrbL: domain 1 of 1, from 33 to 67: score 0.8, E = 8 + *->ksstiesfnlfvllaivllslvlilllkqipgiAqglvgavvtlgga + ++st+ + +++ ++ +++++l+l++ ++iA + blumeria_G 33 AASTLLI-----AVEHIVNCAAFCLALRSSASIA------------- 61 + + vaaalaGG<-* + a+ +GG + blumeria_G 62 --ASNSGG 67 + +TNV_CP: domain 1 of 1, from 58 to 80: score 0.1, E = 7.9 + CS SSSGGGB-TTEEEEEEEES-SS- + *->AdvAaSNgpgAvFvLeigdkvag<-* + A++AaSN g vF+L +++ g + blumeria_G 58 ASIAASNSGGCVFFLPAASSAGG 80 + +DGOK: domain 1 of 1, from 94 to 109: score 0.5, E = 1.3 + *->VdGDeAvrAGLseiAr<-* + VdG A AGL ++ r + blumeria_G 94 VDGVSALFAGLTSAGR 109 + +Peptidase_S29: domain 1 of 1, from 113 to 127: score 4.7, E = 1.1 + *->GevqvLgTaTqsflG<-* + G+v++ + aT+ flG + blumeria_G 113 GTVMRFSGATTVFLG 127 + +DUF1301: domain 1 of 1, from 148 to 157: score 0.4, E = 9.9 + *->gVKvFSlSTS<-* + ++vFS+STS + blumeria_G 148 SARVFSFSTS 157 + +// + +Query sequence: blumeria_Grouper_4152_12:NoCat_2 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +DUF1602 Protein of unknown function (DUF1602) 5.0 0.39 1 +Toxin_18 Conotoxin O-superfamily 4.2 4.4 1 +ABC_transp_aux ABC-type uncharacterized transport sys 1.1 5.2 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +Toxin_18 1/1 21 26 .. 50 55 .] 4.2 4.4 +ABC_transp_aux 1/1 126 137 .. 276 287 .] 1.1 5.2 +DUF1602 1/1 143 159 .. 23 39 .] 5.0 0.39 + +Alignments of top-scoring domains: +Toxin_18: domain 1 of 1, from 21 to 26: score 4.2, E = 4.4 + *->gfCLpr<-* + +fCL+r + blumeria_G 21 NFCLHR 26 + +ABC_transp_aux: domain 1 of 1, from 126 to 137: score 1.1, E = 5.2 + *->wGvrldpdlVlD<-* + wG+r+dp+l+l + blumeria_G 126 WGIRWDPRLALR 137 + +DUF1602: domain 1 of 1, from 143 to 159: score 5.0, E = 0.39 + *->kPPlSSsGalfanplrP<-* + +P l + G+l + +lrP + blumeria_G 143 MPKLNRRGFLASRLLRP 159 + +// + +Query sequence: blumeria_Grouper_4152_12:NoCat_3 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +zf-P11 P-11 zinc finger 3.6 1.8 1 +V-ATPase_G Vacuolar (H+)-ATPase G subunit 2.4 5.3 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +zf-P11 1/1 102 122 .. 1 20 [. 3.6 1.8 +V-ATPase_G 1/1 126 135 .. 1 10 [. 2.4 5.3 + +Alignments of top-scoring domains: +zf-P11: domain 1 of 1, from 102 to 122: score 3.6, E = 1.8 + *->GplnCKs..CWfkdknLveCsd<-* + Gp +C+s+ CW + + L C d + blumeria_G 102 GPHFCRSrxCW-NRDALLGCDD 122 + +V-ATPase_G: domain 1 of 1, from 126 to 135: score 2.4, E = 5.3 + *->sqsqGIQqLL<-* + ++s+GIQ LL + blumeria_G 126 GGSGGIQDLL 135 + +// + +Query sequence: blumeria_Grouper_4152_12:NoCat_4 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +XhoI Restriction endonuclease XhoI 9.9 0.014 1 +Endomucin Endomucin 0.1 6 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +XhoI 1/1 92 122 .. 172 202 .] 9.9 0.014 +Endomucin 1/1 113 119 .. 261 267 .] 0.1 6 + +Alignments of top-scoring domains: +XhoI: domain 1 of 1, from 92 to 122: score 9.9, E = 0.014 + *->klvlerfytrpasllrdaqavlqGiikeprk<-* + ++++ ++yt ++ +d++++ qG k+ ++ + blumeria_G 92 RSSRQKKYTPSRIACSDRSGGAQGKTKSRAI 122 + +Endomucin: domain 1 of 1, from 113 to 119: score 0.1, E = 6 + *->AQGKtKN<-* + AQGKtK + blumeria_G 113 AQGKTKS 119 + +// + +Query sequence: blumeria_Grouper_4152_12:NoCat_5 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +SLT Transglycosylase SLT domain 4.5 1.2 1 +DUF881 Bacterial protein of unknown function 4.0 1.6 1 +DUF2346 Uncharacterized conserved protein (DUF 3.2 2.8 1 +DUF1798 Bacterial domain of unknown function ( 3.0 3.3 1 +LBP_BPI_CETP LBP / BPI / CETP family, N-terminal do 1.8 3.8 1 +Jun Jun-like transcription factor -0.7 6.5 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +DUF1798 1/1 2 19 .. 35 52 .. 3.0 3.3 +DUF881 1/1 46 69 .. 214 237 .] 4.0 1.6 +Jun 1/1 77 93 .. 264 284 .. -0.7 6.5 +SLT 1/1 89 108 .. 1 20 [. 4.5 1.2 +DUF2346 1/1 93 115 .. 63 85 .] 3.2 2.8 +LBP_BPI_CETP 1/1 124 139 .. 191 209 .] 1.8 3.8 + +Alignments of top-scoring domains: +DUF1798: domain 1 of 1, from 2 to 19: score 3.0, E = 3.3 + *->KPfvdevdqllaeWkelA<-* + +P+vd+vd++++++k+lA + blumeria_G 2 VPEVDMVDAEVEKLKTLA 19 + +DUF881: domain 1 of 1, from 46 to 69: score 4.0, E = 1.6 + *->VeksdditiPAydgplklrYAkPv<-* + V + +it+PA++ p +r Ak++ + blumeria_G 46 VAPEKRITVPALPRPAEVRPAKRA 69 + +Jun: domain 1 of 1, from 77 to 93: score -0.7, E = 6.5 + *->qHheNPpgfqhsavgpPRlaa<-* + +++eNPp+ a++pP+l a + blumeria_G 77 AGAENPPL----APQPPALEA 93 + +SLT: domain 1 of 1, from 89 to 108: score 4.5, E = 1.2 + CS HHHHHHHHHHTS-HHHHHHH + *->dliikaaekygidpsllaAi<-* + ++ ++a+ k+ ++p llaAi + blumeria_G 89 PALEAAGRKNTHPPELLAAI 108 + +DUF2346: domain 1 of 1, from 93 to 115: score 3.2, E = 2.8 + *->AtKRrEkhdneLlealeeeEaKk<-* + A R+ h eLl+a+e eE+ + blumeria_G 93 AAGRKNTHPPELLAAIEAEERRA 115 + +LBP_BPI_CETP: domain 1 of 1, from 124 to 139: score 1.8, E = 3.8 + CS HHHHHHHCHHHH...HTTS + *->lCPviessVnslNvhLstl<-* + +C +++ssV++ L++l + blumeria_G 124 ICSTAISSVEAA---LQPL 139 + +// + +Query sequence: blumeria_Grouper_4152_12:NoCat_6 +Accession: [none] +Description: [none] + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +DUF258 Protein of unknown function, DUF258 1.5 3.8 1 +TRAP_alpha Translocon-associated protein (TRAP), alph 0.1 4.1 1 +DUF1289 Protein of unknown function (DUF1289) 2.8 5.3 1 +SOCS_box SOCS box 2.4 9.7 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +DUF258 1/1 50 62 .. 293 305 .] 1.5 3.8 +SOCS_box 1/1 85 90 .. 1 6 [. 2.4 9.7 +DUF1289 1/1 95 115 .. 36 56 .] 2.8 5.3 +TRAP_alpha 1/1 106 116 .. 317 327 .] 0.1 4.1 + +Alignments of top-scoring domains: +DUF258: domain 1 of 1, from 50 to 62: score 1.5, E = 3.8 + CS -HHHHHHHHHHHH + *->seeRYesYlklle<-* + s++R+++Y+ l++ + blumeria_G 50 SASRFQHYRDLQK 62 + +SOCS_box: domain 1 of 1, from 85 to 90: score 2.4, E = 9.7 + *->prSLqh<-* + prSLqh + blumeria_G 85 PRSLQH 90 + +DUF1289: domain 1 of 1, from 95 to 115: score 2.8, E = 5.3 + *->dERravlqllpqRlaalglkp<-* + +E+ + lq+++qR +++++ + + blumeria_G 95 AEKIHTLQNCLQRSKRRSAGQ 115 + +TRAP_alpha: domain 1 of 1, from 106 to 116: score 0.1, E = 4.1 + *->kRkvKRsvGdD<-* + +R +Rs+G+D + blumeria_G 106 QRSKRRSAGQD 116 + +//