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: /db/iprscan/data/Pfam.bin Sequence file: /db/iprscan/tmp/20080812/iprscan-20080812-22363859/chunk_1/iprscan-20080812-22363859.nocrc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query sequence: hk03782 Accession: [none] Description: [none] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- PF00562.18.fs RNA polymerase Rpb2, domain 6 671.0 7e-218 1 PF00562.18.ls RNA polymerase Rpb2, domain 6 673.1 2e-199 1 PF04563.6.fs RNA polymerase beta subunit 347.5 4.4e-106 1 PF04563.6.ls RNA polymerase beta subunit 349.4 5.4e-102 1 PF04561.5.fs RNA polymerase Rpb2, domain 2 312.0 1.8e-99 1 PF04561.5.ls RNA polymerase Rpb2, domain 2 313.8 2.8e-91 1 PF04560.10.fs RNA polymerase Rpb2, domain 7 181.6 2.3e-52 1 PF04560.10.ls RNA polymerase Rpb2, domain 7 183.7 4.3e-52 1 PF04566.3.fs RNA polymerase Rpb2, domain 4 142.8 6.2e-41 1 PF04566.3.ls RNA polymerase Rpb2, domain 4 144.8 2.1e-40 1 PF04565.7.fs RNA polymerase Rpb2, domain 3 106.8 1.3e-29 1 PF04565.7.ls RNA polymerase Rpb2, domain 3 108.7 1.6e-29 1 PF04567.7.fs RNA polymerase Rpb2, domain 5 89.8 8.6e-29 1 PF04567.7.ls RNA polymerase Rpb2, domain 5 91.4 2.5e-24 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- PF04563.6.ls 1/1 50 463 .. 1 229 [] 349.4 5.4e-102 PF04563.6.fs 1/1 50 463 .. 1 229 [] 347.5 4.4e-106 PF04561.5.fs 1/1 213 406 .. 1 223 [] 312.0 1.8e-99 PF04561.5.ls 1/1 213 406 .. 1 223 [] 313.8 2.8e-91 PF04565.7.fs 1/1 480 545 .. 1 71 [] 106.8 1.3e-29 PF04565.7.ls 1/1 480 545 .. 1 71 [] 108.7 1.6e-29 PF04566.3.fs 1/1 579 642 .. 1 64 [] 142.8 6.2e-41 PF04566.3.ls 1/1 579 642 .. 1 64 [] 144.8 2.1e-40 PF04567.7.fs 1/1 665 712 .. 1 78 [] 89.8 8.6e-29 PF04567.7.ls 1/1 665 712 .. 1 78 [] 91.4 2.5e-24 PF00562.18.fs 1/1 717 1092 .. 1 363 [] 671.0 7e-218 PF00562.18.ls 1/1 717 1092 .. 1 363 [] 673.1 2e-199 PF04560.10.fs 1/1 1094 1186 .] 1 92 [] 181.6 2.3e-52 PF04560.10.ls 1/1 1094 1186 .] 1 92 [] 183.7 4.3e-52 Alignments of top-scoring domains: PF04563.6.ls: domain 1 of 1, from 50 to 463: score 349.4, E = 5.4e-102 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx *->gLVrqQldSFneFldegLqnseeiidefspIededeaQhttesgnle gLVrqQldSF+eF+++ +q +i+++ +pI ++ eaQh+ + +++ hk03782 50 GLVRQQLDSFDEFIQMSVQ---RIVEDAPPIDLQAEAQHASGEVEEP 93 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx iefslkfgqiklakPkikedVsDgktreiyPqeARlRnlTYSsplYVpve +++ lkf+qi+l+kP+++e Dg + +++P+eARlRnlTYS+plYV+++ hk03782 94 PRYLLKFEQIYLSKPTHWE--RDGAPSPMMPNEARLRNLTYSAPLYVDIT 141 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ltvnntdddgevseeeiekekVfiGkiPlMLrskaCiLnglseselaklg +tv + ++ + +++k fiGkiP+MLrs++C Lngl++++l +l+ hk03782 142 KTVIKE----GEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELN 187 RF xxxxxxxxxxxxxxxxxxxxxxxxx EcplDpGGyFIvNGsEKVIiaQirr......................... EcplDpGGyFI+NGsEKV+iaQ+++ + +++++ ++ ++ hk03782 188 ECPLDPGGYFIINGSEKVLIAQEKMatntvyvfakkdskyaytgecrscl 237 RF .................................................. ++++++ + + +++ + +++ + + + + + + + hk03782 238 enssrptstiwvsmlarggqgakksaigqrivatlpyikqevpiiivfra 287 RF .................................................. + ++++ ++ + ++++ + +++ ++ + + + ++++ hk03782 288 lgfvsdrdilehiiydfedpemmemvkpsldeafviqeqnvalnfigsrg 337 RF .................................................. +++ ++++ + ++ ++ ++ + ++ + ++ + ++ hk03782 338 akpgvtkekrikyakevlqkemlphvgvsdfcetkkayflgymvhrllla 387 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxx ......................eLLqslFrilLnrLekdvrerlqkclkk ++++ +++++ ++++ + ++LL+ lFr +++L k+vr + qk +++ hk03782 388 algrrelddrdhygnkrldlagPLLAFLFRGMFKNLLKEVRIYAQKFIDR 437 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxx krkkdftltnlVnsnkpItsglryflatG<-* ++ df+l ++++ ++I++gl+y+latG hk03782 438 GK--DFNLELAIKT-RIISDGLKYSLATG 463 PF04563.6.fs: domain 1 of 1, from 50 to 463: score 347.5, E = 4.4e-106 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx *->gLVrqQldSFneFldegLqnseeiidefspIededeaQhttesgnle gLVrqQldSF+eF+++ +q +i+++ +pI ++ eaQh+ + +++ hk03782 50 GLVRQQLDSFDEFIQMSVQ---RIVEDAPPIDLQAEAQHASGEVEEP 93 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx iefslkfgqiklakPkikedVsDgktreiyPqeARlRnlTYSsplYVpve +++ lkf+qi+l+kP+++e Dg + +++P+eARlRnlTYS+plYV+++ hk03782 94 PRYLLKFEQIYLSKPTHWE--RDGAPSPMMPNEARLRNLTYSAPLYVDIT 141 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ltvnntdddgevseeeiekekVfiGkiPlMLrskaCiLnglseselaklg +tv + ++ + +++k fiGkiP+MLrs++C Lngl++++l +l+ hk03782 142 KTVIKE----GEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELN 187 RF xxxxxxxxxxxxxxxxxxxxxxxxx EcplDpGGyFIvNGsEKVIiaQirr......................... EcplDpGGyFI+NGsEKV+iaQ+++ + +++++ ++ ++ hk03782 188 ECPLDPGGYFIINGSEKVLIAQEKMatntvyvfakkdskyaytgecrscl 237 RF .................................................. ++++++ + + +++ + +++ + + + + + + + hk03782 238 enssrptstiwvsmlarggqgakksaigqrivatlpyikqevpiiivfra 287 RF .................................................. + ++++ ++ + ++++ + +++ ++ + + + ++++ hk03782 288 lgfvsdrdilehiiydfedpemmemvkpsldeafviqeqnvalnfigsrg 337 RF .................................................. +++ ++++ + ++ ++ ++ + ++ + ++ + ++ hk03782 338 akpgvtkekrikyakevlqkemlphvgvsdfcetkkayflgymvhrllla 387 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxx ......................eLLqslFrilLnrLekdvrerlqkclkk ++++ +++++ ++++ + ++LL+ lFr +++L k+vr + qk +++ hk03782 388 algrrelddrdhygnkrldlagPLLAFLFRGMFKNLLKEVRIYAQKFIDR 437 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxx krkkdftltnlVnsnkpItsglryflatG<-* ++ df+l ++++ ++I++gl+y+latG hk03782 438 GK--DFNLELAIKT-RIISDGLKYSLATG 463 PF04561.5.fs: domain 1 of 1, from 213 to 406: score 312.0, E = 1.8e-99 *->rsngiyvekeldkngiy.aEvRsqaesssgllsatytsslisnrgsw ++n +yv++++d ++ y++E+Rs++e+ss+++s++++s+l++++ + hk03782 213 ATNTVYVFAKKDSKYAYtGECRSCLENSSRPTSTIWVSMLARGGQGA 259 lklekdgktliwtrpsikrkIPivivLrALGlvsDrEILdricYnsfVke k +++++ +t+p+ik+++Pi+iv+rALG+vsDr+IL++i+Y hk03782 260 KKSAIGQRIV-ATLPYIKQEVPIIIVFRALGFVSDRDILEHIIY------ 302 dfndpqmleelkpeleeaeniytqeeALdyIGkHFKeRgvalrrgeepri df+dp+m+e++kp+l ea++i+ q++AL++IG+ Rg ++++ +e+ri hk03782 303 DFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGS----RGAKPGVTKEKRI 348 qrareiLqsrfFDpkRYdLGiigRenLnkHLglnepfenkrvlKaqdily ++a+e+Lq +e+L+ H+g++ ++e+k Ka++++y hk03782 349 KYAKEVLQ---------------KEMLP-HVGVSDFCETK---KAYFLGY 379 midrLLllklGrrepDDiDHlgNKRvr<-* m++rLLl++lGrre+DD+DH+gNKR++ hk03782 380 MVHRLLLAALGRRELDDRDHYGNKRLD 406 PF04561.5.ls: domain 1 of 1, from 213 to 406: score 313.8, E = 2.8e-91 *->rsngiyvekeldkngiy.aEvRsqaesssgllsatytsslisnrgsw ++n +yv++++d ++ y++E+Rs++e+ss+++s++++s+l++++ + hk03782 213 ATNTVYVFAKKDSKYAYtGECRSCLENSSRPTSTIWVSMLARGGQGA 259 lklekdgktliwtrpsikrkIPivivLrALGlvsDrEILdricYnsfVke k +++++ +t+p+ik+++Pi+iv+rALG+vsDr+IL++i+Y hk03782 260 KKSAIGQRIV-ATLPYIKQEVPIIIVFRALGFVSDRDILEHIIY------ 302 dfndpqmleelkpeleeaeniytqeeALdyIGkHFKeRgvalrrgeepri df+dp+m+e++kp+l ea++i+ q++AL++IG+ Rg ++++ +e+ri hk03782 303 DFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGS----RGAKPGVTKEKRI 348 qrareiLqsrfFDpkRYdLGiigRenLnkHLglnepfenkrvlKaqdily ++a+e+Lq +e+L+ H+g++ ++e+k Ka++++y hk03782 349 KYAKEVLQ---------------KEMLP-HVGVSDFCETK---KAYFLGY 379 midrLLllklGrrepDDiDHlgNKRvr<-* m++rLLl++lGrre+DD+DH+gNKR++ hk03782 380 MVHRLLLAALGRRELDDRDHYGNKRLD 406 PF04565.7.fs: domain 1 of 1, from 480 to 545: score 106.8, E = 1.3e-29 *->QvldqtNplselshkRrvsrlGPGglsrerktfevRdlhpsqyGriC Qvl+++++ s+lsh+Rr++ +++ r+ k ++R+lh++ +G++C hk03782 480 QVLNRLTFASTLSHLRRLN----SPIGRDGKLAKPRQLHNTLWGMVC 522 PieTPErGqncGLvnsLalyarin<-* P+eTPE G ++GLv++Lal+a+i+ hk03782 523 PAETPE-GHAVGLVKNLALMAYIS 545 PF04565.7.ls: domain 1 of 1, from 480 to 545: score 108.7, E = 1.6e-29 *->QvldqtNplselshkRrvsrlGPGglsrerktfevRdlhpsqyGriC Qvl+++++ s+lsh+Rr++ +++ r+ k ++R+lh++ +G++C hk03782 480 QVLNRLTFASTLSHLRRLN----SPIGRDGKLAKPRQLHNTLWGMVC 522 PieTPErGqncGLvnsLalyarin<-* P+eTPE G ++GLv++Lal+a+i+ hk03782 523 PAETPE-GHAVGLVKNLALMAYIS 545 PF04566.3.fs: domain 1 of 1, from 579 to 642: score 142.8, E = 6.2e-41 *->VYvNGklvGthrnPeeLvetlRelRRkGkissqevsivrnirqreir ++vNG++vG+h++Pe+L++tlR+lRR+++i+ +evs++r+ir+reir hk03782 579 IFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIR 625 InTDaGRicRPLiIVeN<-* I+TDaGRicRPL+IVe hk03782 626 IYTDAGRICRPLLIVEK 642 PF04566.3.ls: domain 1 of 1, from 579 to 642: score 144.8, E = 2.1e-40 *->VYvNGklvGthrnPeeLvetlRelRRkGkissqevsivrnirqreir ++vNG++vG+h++Pe+L++tlR+lRR+++i+ +evs++r+ir+reir hk03782 579 IFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIR 625 InTDaGRicRPLiIVeN<-* I+TDaGRicRPL+IVe hk03782 626 IYTDAGRICRPLLIVEK 642 PF04567.7.fs: domain 1 of 1, from 665 to 712: score 89.8, E = 8.6e-29 *->wddLlkeGPHviEYlDaEEEEtamIamtpeDLe.srqmkagyeieee w+dL+++G v+EY+D+ EEEt+m amtp+DL ++ hk03782 665 WQDLVASG--VVEYIDTLEEETVMLAMTPDDLQeK------------ 697 dedpgiedpnrRvkpkpneeithtyTHcEIhP<-* + +++ tyTHcEIhP hk03782 698 -----------------EVAYCSTYTHCEIHP 712 PF04567.7.ls: domain 1 of 1, from 665 to 712: score 91.4, E = 2.5e-24 *->wddLlkeGPHviEYlDaEEEEtamIamtpeDLe.srqmkagyeieee w+dL+++G v+EY+D+ EEEt+m amtp+DL ++ hk03782 665 WQDLVASG--VVEYIDTLEEETVMLAMTPDDLQeK------------ 697 dedpgiedpnrRvkpkpneeithtyTHcEIhP<-* + +++ tyTHcEIhP hk03782 698 -----------------EVAYCSTYTHCEIHP 712 PF00562.18.fs: domain 1 of 1, from 717 to 1092: score 671.0, E = 7e-218 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx *->gvvAsligfvehnqSprityqcamgKQaigypllnyqiRsDqgtcll gv+As+i+f++hnqSpr+tyq+amgKQa+g++++n+ R+D+++++l hk03782 717 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVL 763 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx qyPqvplvetvtkgqilaDGPatenGelplGqNalVAvmsyeGYNyEDAi +yPq+plv+t++++++ + elp+G+N +VA+ sy+GYN+ED++ hk03782 764 YYPQKPLVTTRSMEYLRFR-------ELPAGINSIVAIASYTGYNQEDSV 806 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx iiNkrlvergvytSihieeyeiearktklggpEeitrpipnvrggvseaa i+N+++v+rg+++S+++++y+ +++k+ ++E +++p++++++g+++a hk03782 807 IMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAI 856 RF xxxxxxxxxxxxxxxxxxxxxxxxx lrkLDedGIvrvGaeVkpGDiLvGK......................... ++kLD+dG++++G +V ++D+++GK+ + ++++++ ++++++ ++++ ++ hk03782 857 YDKLDDDGLIAPGVRVSGDDVIIGKtvtlpenedelestnrrytkrdcst 906 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ...............enGDelneggngvnklvkVyvrqkRkpqiGDKfAs ++++++ ++ + ln++g k++k++vr++R+pqiGDKfAs hk03782 907 flrtsetgivdqvmvT----LNQEGY---KFCKIRVRSVRIPQIGDKFAS 949 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RHGQKGViSkivPqeDMPFledGtppDIIlNPhGvPSRMTiGQllEcllG RHGQKG++++ ++qeDMPF+++G++pDII+NPh++PSRMTiG+l+Ecl G hk03782 950 RHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQG 999 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx kAgallGkrvdgtpFdepvfdeasvedisekLkeaGfnysgWlFeenhpG k++a++G+ +d+tpF + ++v+ is+ L ++G+ +g hk03782 1000 KVSANKGEIGDATPFND----AVNVQKISNLLSDYGYHLRG--------- 1036 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx KevLYDGrTGepfeapIfvGviYYqKLkHMVdDKiHARStGPysllTqQP +evLY+G+TG+++ +If+G++YYq+LkHMVdDKiH+R++GP+++l +QP hk03782 1037 NEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQP 1086 RF xxxxxx lgGRar<-* +GR+r hk03782 1087 MEGRSR 1092 PF00562.18.ls: domain 1 of 1, from 717 to 1092: score 673.1, E = 2e-199 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx *->gvvAsligfvehnqSprityqcamgKQaigypllnyqiRsDqgtcll gv+As+i+f++hnqSpr+tyq+amgKQa+g++++n+ R+D+++++l hk03782 717 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVL 763 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx qyPqvplvetvtkgqilaDGPatenGelplGqNalVAvmsyeGYNyEDAi +yPq+plv+t++++++ + elp+G+N +VA+ sy+GYN+ED++ hk03782 764 YYPQKPLVTTRSMEYLRFR-------ELPAGINSIVAIASYTGYNQEDSV 806 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx iiNkrlvergvytSihieeyeiearktklggpEeitrpipnvrggvseaa i+N+++v+rg+++S+++++y+ +++k+ ++E +++p++++++g+++a hk03782 807 IMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAI 856 RF xxxxxxxxxxxxxxxxxxxxxxxxx lrkLDedGIvrvGaeVkpGDiLvGK......................... ++kLD+dG++++G +V ++D+++GK+ + ++++++ ++++++ ++++ ++ hk03782 857 YDKLDDDGLIAPGVRVSGDDVIIGKtvtlpenedelestnrrytkrdcst 906 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ...............enGDelneggngvnklvkVyvrqkRkpqiGDKfAs ++++++ ++ + ln++g k++k++vr++R+pqiGDKfAs hk03782 907 flrtsetgivdqvmvT----LNQEGY---KFCKIRVRSVRIPQIGDKFAS 949 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RHGQKGViSkivPqeDMPFledGtppDIIlNPhGvPSRMTiGQllEcllG RHGQKG++++ ++qeDMPF+++G++pDII+NPh++PSRMTiG+l+Ecl G hk03782 950 RHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQG 999 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx kAgallGkrvdgtpFdepvfdeasvedisekLkeaGfnysgWlFeenhpG k++a++G+ +d+tpF + ++v+ is+ L ++G+ +g hk03782 1000 KVSANKGEIGDATPFND----AVNVQKISNLLSDYGYHLRG--------- 1036 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx KevLYDGrTGepfeapIfvGviYYqKLkHMVdDKiHARStGPysllTqQP +evLY+G+TG+++ +If+G++YYq+LkHMVdDKiH+R++GP+++l +QP hk03782 1037 NEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQP 1086 RF xxxxxx lgGRar<-* +GR+r hk03782 1087 MEGRSR 1092 PF04560.10.fs: domain 1 of 1, from 1094 to 1186: score 181.6, E = 2.3e-52 *->GGqRFGEMEvWALeAyGAAytLqErLtikSDayevdvcgrcgayaaa GG+RFGEME+++ +A+GAA++L+ErL++ SD+y+v+vc+ cg++a+a hk03782 1094 GGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIA 1140 nkrkn.yeCrickgktiiepgtiPEsFKlLlqELqSLgldirlyle<-* n r+++yeCr c++kt+i+ +++P+++KlL+qEL+S+ +++r++ + hk03782 1141 NTRTHtYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV 1186 PF04560.10.ls: domain 1 of 1, from 1094 to 1186: score 183.7, E = 4.3e-52 *->GGqRFGEMEvWALeAyGAAytLqErLtikSDayevdvcgrcgayaaa GG+RFGEME+++ +A+GAA++L+ErL++ SD+y+v+vc+ cg++a+a hk03782 1094 GGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIA 1140 nkrkn.yeCrickgktiiepgtiPEsFKlLlqELqSLgldirlyle<-* n r+++yeCr c++kt+i+ +++P+++KlL+qEL+S+ +++r++ + hk03782 1141 NTRTHtYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV 1186 //