Mercurial > repos > yufei-luo > s_mart
diff commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/test_hmmpfam_output @ 31:0ab839023fe4
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 14:33:21 -0400 |
| parents | 94ab73e8a190 |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/test_hmmpfam_output Tue Apr 30 14:33:21 2013 -0400 @@ -0,0 +1,321 @@ +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: myhmms +Sequence file: test.fa +- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +Query sequence: pkinase_full +Accession: [none] +Description: Dario rerio + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +pkinase Protein kinase domain 266.6 3.3e-80 1 +pkinase Protein kinase domain 265.4 7.6e-80 1 +rrm -42.5 2.5 1 +rrm -8.7 3.7 1 +fn3 Fibronectin type III domain -45.8 3.7 1 +fn3 Fibronectin type III domain -9.0 3.8 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +rrm 1/1 169 180 .. 66 77 .] -8.7 3.7 +fn3 1/1 197 200 .. 81 84 .] -9.0 3.8 +rrm 1/1 256 319 .. 1 77 [] -42.5 2.5 +pkinase 1/1 258 540 .. 1 294 [] 266.6 3.3e-80 +pkinase 1/1 258 537 .. 1 289 [. 265.4 7.6e-80 +fn3 1/1 434 506 .. 1 84 [] -45.8 3.7 + +Alignments of top-scoring domains: +rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7 + *->nGkelggrklrv<-* + n++ ++l v + pkinase_fu 169 NKQDPHQHRLSV 180 + +fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8 + CS CCCC + *->GpeS<-* + G eS + pkinase_fu 197 GGES 200 + +rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5 + *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks + +N++ +d+ e + F+ + +++ + + pkinase_fu 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285 + + kGfaFVeFeseedAekAlealnG.kelggrklrv<-* + + V++ +ee+ ++ ++++ + l++ + + pkinase_fu 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319 + +pkinase: domain 1 of 1, from 258 to 540: score 266.6, E = 3.3e-80 + *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek + +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ + pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 + + .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr + ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr + pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 + + ng........................gplsekeakkialQilrGleYLHs + + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL + + pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402 + + ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY + +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p + + pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451 + + mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev + +m+PE ++++ y+s++DvW++Gv+L+E++++g + pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483 + + dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd + ++P+++ + ee+ + +++ g l +p+nc+ el+ + pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517 + + LlkkcLnkDPskRpGsatakeilnhpwf<-* + L++ c+ P++Rp ++ i h + + pkinase_fu 518 LMRLCWSGHPTDRP---SFASI--HRIL 540 + +pkinase: domain 1 of 1, from 258 to 537: score 265.4, E = 7.6e-80 + *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek + +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ + pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 + + .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr + ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr + pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 + + ng........................gplsekeakkialQilrGleYLHs + + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL + + pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402 + + ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY + +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p + + pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451 + + mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev + +m+PE ++++ y+s++DvW++Gv+L+E++++g + pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483 + + dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd + ++P+++ + ee+ + +++ g l +p+nc+ el+ + pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517 + + LlkkcLnkDPskRpGsatakeil<-* + L++ c+ P++Rp ++ i+ + pkinase_fu 518 LMRLCWSGHPTDRP---SFASIH 537 + +fn3: domain 1 of 1, from 434 to 506: score -45.8, E = 3.7 + CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.E + *->PsaPtnltvtdvtstsltlsWsppt........gngpitgYevtyRq + a ++++ + + ++W pp++ ++ + +++ Y v + + + pkinase_fu 434 IYAADYYKASE--NDAIPIRWMPPEsifynrytSESDVWAYGVVL-W 477 + + CS CCCCCC CCCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC + pkngge..wneltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-* + + + + ++ + ++V+ +g+ S + pkinase_fu 478 EIFSYGmqPYYGMAHEEV--------------IYYVR--DGN--VLS 506 + +// + +Query sequence: pkinase_part +Accession: [none] +Description: Dario rerio + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +pkinase Protein kinase domain 101.5 1.7e-30 1 +pkinase Protein kinase domain -94.7 1.5e-05 1 +rrm -42.5 2.5 1 +rrm -8.7 3.7 1 +fn3 Fibronectin type III domain -9.0 3.8 1 +fn3 Fibronectin type III domain -52.2 5.9 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +rrm 1/1 169 180 .. 66 77 .] -8.7 3.7 +fn3 1/1 197 200 .. 81 84 .] -9.0 3.8 +fn3 1/1 233 299 .. 1 84 [] -52.2 5.9 +rrm 1/1 256 319 .. 1 77 [] -42.5 2.5 +pkinase 1/1 258 400 .] 1 116 [. 101.5 1.7e-30 +pkinase 1/1 258 400 .] 1 294 [] -94.7 1.5e-05 + +Alignments of top-scoring domains: +rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7 + *->nGkelggrklrv<-* + n++ ++l v + pkinase_pa 169 NKQDPHQHRLSV 180 + +fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8 + CS CCCC + *->GpeS<-* + G eS + pkinase_pa 197 GGES 200 + +fn3: domain 1 of 1, from 233 to 299: score -52.2, E = 5.9 + CS CCCC CEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC + *->PsaP.tnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew + P + ++l ++ +s ls + p + i++ +R + ++g + pkinase_pa 233 PNPMyQRL---PLLLNSKLLSLEYP--RNNIEY----VR-DIGEG-- 267 + + CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC + neltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-* + g ++ gL P + ++ + + ++S + pkinase_pa 268 ----AFGRVFQARAPGLLPTEPFTMVAVKMLKE--EAS 299 + +rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5 + *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks + +N++ +d+ e + F+ + +++ + + pkinase_pa 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285 + + kGfaFVeFeseedAekAlealnG.kelggrklrv<-* + + V++ +ee+ ++ ++++ + l++ + + pkinase_pa 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319 + +pkinase: domain 1 of 1, from 258 to 400: score 101.5, E = 1.7e-30 + *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek + +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ + pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 + + .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr + ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr + pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 + + ng........................gplsekeakkialQilrGleYL<- + + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL + pkinase_pa 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYL 400 + + * + + pkinase_pa - - + +pkinase: domain 1 of 1, from 258 to 400: score -94.7, E = 1.5e-05 + *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek + +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++ + pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303 + + .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr + ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr + pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352 + + nggplsekeakkialQilrGleYLHsngivHRDLKpeNILldendgtvKi + + + pkinase_pa 353 RC------------------------------------------------ 354 + + aDFGLArllesssklttfvGTpwYmmAPEvilegrgysskvDvWSlGviL + A++ s + +t++ ++ PE + pkinase_pa 355 -----ATQQP-SLSRDTLTSSSLVS-EPER-------------------- 377 + + yElltggplfpgadlpaftggdevdqliifvlklPfsdelpktridplee + +P s + pkinase_pa 378 --------------------------------YPPLS------------- 382 + + lfriikrpglrlplpsncSeelkdLlkkcLnkDPskRpGsatakeilnhp + + + ++S+ + + + pkinase_pa 383 -----CQ------EQLSISKQVAAGM-----------A------------ 398 + + wf<-* + ++ + pkinase_pa 399 YL 400 + +// + +Query sequence: S13421 +Accession: [none] +Description: S13421 GLOBIN - BRINE SHRIMP, 1405 bases, EDBC29AF checksum. + +Scores for sequence family classification (score includes all domains): +Model Description Score E-value N +-------- ----------- ----- ------- --- +pkinase Protein kinase domain -171.6 0.19 1 +rrm -32.5 0.26 1 +rrm -6.1 0.92 1 +fn3 Fibronectin type III domain -39.7 1.2 1 +pkinase Protein kinase domain -9.2 1.8 1 +fn3 Fibronectin type III domain -7.5 1.9 1 + +Parsed for domains: +Model Domain seq-f seq-t hmm-f hmm-t score E-value +-------- ------- ----- ----- ----- ----- ----- ------- +fn3 1/1 143 224 .. 1 84 [] -39.7 1.2 +pkinase 1/1 233 241 .. 1 9 [. -9.2 1.8 +rrm 1/1 440 456 .. 1 17 [. -6.1 0.92 +rrm 1/1 669 731 .. 1 77 [] -32.5 0.26 +pkinase 1/1 906 1127 .. 1 294 [] -171.6 0.19 +fn3 1/1 923 934 .. 1 12 [. -7.5 1.9 + +Alignments of top-scoring domains: +fn3: domain 1 of 1, from 143 to 224: score -39.7, E = 1.2 + CS C CCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC + *->P.saPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew + + ++t+l++ dv ++ sWs+ +g+ + tg v R + ng + + S13421 143 IdLEVTGLSCVDVAN--IQESWSKVSGDLKTTGSVVFQR-MINGH-P 185 + + CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC + neltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-* + +++ ++ + + l L + + V v ++ +G + S13421 186 EYQQLFRQFRDVDLDKLGESNSFVAHVFRVVAAFdGIIH 224 + +pkinase: domain 1 of 1, from 233 to 241: score -9.2, E = 1.8 + *->yelleklGe<-* + +l+klGe + S13421 233 VSTLKKLGE 241 + +rrm: domain 1 of 1, from 440 to 456: score -6.1, E = 0.92 + *->lfVgNLppdvteedLkd<-* + + ++ L++ + d+ d + S13421 440 VIISFLNEGLRQADIVD 456 + +rrm: domain 1 of 1, from 669 to 731: score -32.5, E = 0.26 + *->lfVgNL.ppdvteedLkdlFskfGpivsikivkDhkektketgkskG + V L+++d+ + + f i k++ D + + S13421 669 --VEELpSTDAFHYHISLVMNRFSSI--GKVIDD------------N 699 + + faFVeFeseedAekAlealnGkelggr.klrv<-* + + FV ++ + e+ ++ l k+++ +l++ + S13421 700 VSFVYLLKKLGREHIKRGLSRKQFDQFvELYI 731 + +pkinase: domain 1 of 1, from 906 to 1127: score -171.6, E = 0.19 + *->yelleklGeGsfGkVykakhkd........ktgkiVAvKilkkekes + ++l G++ ++ + ++ ++ ++ + ++VAv + ++ + S13421 906 FKLMH-------GVIEEGLLQLerinpitgLSAREVAVVKQ---TWN 942 + + ikekrflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdy + + + L+ ++ fe + + v++ +d + S13421 943 LVK----------PDLMGVGMRIFKSLFE-AFPAYQAVFPKFSD-VPLDK 980 + + lrrng....gplsekeakkialQilrGleYLHsngivHRDLKpeNILlde + l + +++ +s ++ Q+ lde + S13421 981 LEDTPavgkHSISVTTKLDELIQT-----------------------LDE 1007 + + ndgtvKiaDFGLArlle........sssklttfvGTpwYmmAPEvi...l + + ++ + LAr+l +++ + + +++++f+ +++ ++++l + S13421 1008 P-ANLAL----LARQLGedhivlrvNKPMFKSFGKVLVRL-----LendL 1047 + + egrgysskvDvW..SlGviLyElltggplfpgadlpaftggdevdqliif + +r s ++ W++++ vi+ ++ g + S13421 1048 GQRFSSFASRSWhkAYDVIVEYIEEG------------------------ 1073 + + vlklPfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcL + l++ +++ dp + + k l + ++++ ++l+ L +k++ + S13421 1074 -LQQSYKQ-------DPVTGITDAEKA--LVQESWDLLKPDLLGLGRKIF 1113 + + nkDPskRpGsatakeilnhpwf<-* + +k +k p +i f + S13421 1114 TKVFTKHP----DYQI----LF 1127 + +fn3: domain 1 of 1, from 923 to 934: score -7.5, E = 1.9 + CS CCCCCEEEEEEC + *->PsaPtnltvtdv<-* + + t+l++++v + S13421 923 INPITGLSAREV 934 + +// +