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view commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/test_hmmpfam_output @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
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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 //