|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
18-1204 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1275.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 18 WTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDdstltldqyaqhTGAQGDVTRRYEINFGQIYLSRPTMTEADGSTT 97
Cdd:PRK08565 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE------------FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSER 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 98 TMFPQEARLRNLTYSSPLYVDMRkkvmVAADSnvpigeeewlveeEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDL 177
Cdd:PRK08565 70 PITPMEARLRNLTYAAPLYLTMI----PVENG-------------IEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEI 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 178 NECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSAlERGSRLISSMQIKlmarnteNSGqTIRA 257
Cdd:PRK08565 133 GEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISS-RAGYRAQVTVERR-------KDG-TIYV 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 258 TLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPndfQMLEMMKPCIEEAF-VIQDKDIALDYIGKRgSTTGVTREKRLR 336
Cdd:PRK08565 204 SFPAVPGKIPFVILMRALGLETDRDIVYAVSLDP---EIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIE 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 337 YAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYK 416
Cdd:PRK08565 280 RAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKY 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 417 YMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDqkrsmvNRVGVSQVLNRYTFASTLSHLRRTNTPIGRDGKLAK 496
Cdd:PRK08565 360 QLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVG------GRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFE 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 497 PRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVH 576
Cdd:PRK08565 434 ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYH 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 577 RDPAHLTETLRSLRRRLDISAEVSI--VRDIREKELRLFTDAGRICRPLFIVDNnpnserrGELCIRKEHIQQLiedkDR 654
Cdd:PRK08565 514 PDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKL----KK 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 655 YDIDpeqrfgWTALVSSGLIEYLDAEEEETVMIAMSPEDLeasrqmqagyeVKEeldpaqrvkpapnphvHawTHCEIHP 734
Cdd:PRK08565 583 GELT------FDDLVKMGVIEYLDAEEEENAYVALDPEDL-----------TPE----------------H--THLEIWP 627
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 735 AMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIV 814
Cdd:PRK08565 628 PAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVV 707
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 815 AILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPvrSTTLRMKHG--TYDKLEDDGLIAPGT 892
Cdd:PRK08565 708 AVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEV 785
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 893 RVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASR 972
Cdd:PRK08565 786 EVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASR 865
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 973 HGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHG 1052
Cdd:PRK08565 866 HGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLG 945
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1053 FQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGC 1132
Cdd:PRK08565 946 YKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGA 1025
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 63054498 1133 SSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRL 1204
Cdd:PRK08565 1026 AMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRL 1097
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
30-1205 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 1180.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 30 LARQQLFSFDEFVQNTMQEIVDDDSTLTLDqyaqhtgaqgDVTRRYEINFGQIYLSRPTMTEaDGSTTTMFPQEARLRNL 109
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDT----------DDDGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 110 TYSSPLYVDMRKKVMvaadsnvpigeeewlvEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFI 189
Cdd:cd00653 70 TYSAPLYVDIRLTVN----------------DKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFI 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 190 INGSEKVIIAQERSAANIVQVFkkaaPSPIAYVAEIRSALERGSRLISSMQIKLMARNtensgQTIRATLPYIRsdipiv 269
Cdd:cd00653 134 INGTEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK-----DRIYVRIDLKR------ 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 270 ivfralgvvpdrdilehicydpndfqmlemmkpcieeafviqdKDIALDYIGKRGsttgvtrekrlryahdilqkellph 349
Cdd:cd00653 199 -------------------------------------------QEEALKYIGKRF------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 350 ittmegfetrkaFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREFN 429
Cdd:cd00653 211 ------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT 278
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 430 LTLAVKSNIITNGLRYSLATGNWGDqKRSMVNRVGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGMV 508
Cdd:cd00653 279 PQLLINSKPITSGIKEFLATGNWGS-KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRI 357
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 509 CPAETPEGQACGLVKNLSLMSYVSvgspsapiiefleewgletledynpsaspnatkvfvngvwlgvhrdpahltetlrs 588
Cdd:cd00653 358 CPIETPEGENCGLVKNLALMARIS-------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 589 lrrrldisaevsivrdirekelrlftdaGRICRPLFIVDNNpnserrgelcirkehiqqliedkdrydidpeqrfgwtal 668
Cdd:cd00653 382 ----------------------------GRIERPYRIVEKE--------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 669 vssglieyldaeeeetvmiamspedleasrqmqagyevkeeldpaqrvkpapnphvhaWTHCEIHPAMILGILASIIPFP 748
Cdd:cd00653 395 ----------------------------------------------------------VTHIEISPSQILSVAASLIPFP 416
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 749 DHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSI 828
Cdd:cd00653 417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 829 IMNQASIDRGLFRSIFYRTYTDQEKKIGMTvmeeFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIP 908
Cdd:cd00653 497 IINKSSVDRGFFRSIHYKKYEIELRKTKNG----PEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 909 LDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTT---NQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRH 985
Cdd:cd00653 573 ETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQ 652
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 986 EDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGH 1065
Cdd:cd00653 653 EDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGR 732
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSD 1145
Cdd:cd00653 733 TGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSD 812
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1146 AYRVIVCDICGLIAIASYkkdsyeCRSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLF 1205
Cdd:cd00653 813 DVVARVCVKCGIILSANL------CRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
566-1204 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 769.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 566 VFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNnpnserrGELCIRKEHI 645
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 646 QQLiedkdrydidPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLeasrqmqagyevkeeldpaqrvkpAPNphvH 725
Cdd:TIGR03670 74 EKL----------KEGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL------------------------TPE---H 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 726 awTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRE 805
Cdd:TIGR03670 117 --THLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDD 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 806 LPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPvrSTTLRMKHG--TYDKLE 883
Cdd:TIGR03670 195 RPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGeeAYKHLD 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 884 DDGLIAPGTRVSGEDIIIGKTAPiPL---DHEELGQRTQlhAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRST 960
Cdd:TIGR03670 273 EDGIVYPEVEVKGGDVLIGKTSP-PRfleELREFGLVTE--RRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDL 349
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 961 RIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVT 1040
Cdd:TIGR03670 350 RIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEP 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1041 VEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFG 1120
Cdd:TIGR03670 430 EEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFG 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1121 EMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI 1200
Cdd:TIGR03670 510 EMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGI 589
|
....
gi 63054498 1201 APRL 1204
Cdd:TIGR03670 590 SPRL 593
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
21-1208 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 719.58 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 21 ISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTldqyaqhtgaqgDVTRRYEINFGQIYLSRPTMTeadgstttmf 100
Cdd:COG0085 7 IKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE------------DFTGNLSLEFGDYRLGEPKYT---------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 101 PQEARLRNLTYSSPLYVDMRkkvmVAADSNVPIgeeewlveeedeEPSKVFIGKIPIMLRStfcilngvsdselydlnec 180
Cdd:COG0085 65 PEECKERDLTYAAPLYVKVR----LVNKETGEI------------KEQEVFMGDFPLMTDS------------------- 109
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 181 pydqgGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSAleRGSRLIssmqIKLMARNTensgqtIRATLP 260
Cdd:COG0085 110 -----GTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLE----FETDKDGT------IYVRID 172
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 261 YIRsDIPIVIVFRALGVVPDRDILEHICYDPNDfqmlEMMKPCIEEAfVIQDKDIALDYIGKR---GSTtgVTREKRLRY 337
Cdd:COG0085 173 RKR-KIPVTVLLRALGLETDEEILEAFGDDPIQ----EYILATLEKD-NTKTQEEALLEIYRKlrpGEP--PTIERAEQL 244
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 338 AHDILQKEL---LPHI---------TTMEGFETR--KAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLF 403
Cdd:COG0085 245 LDNLFFDPKrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQF 324
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 404 RMLFRKMTRDVyKY-MqkcvETNREFNLTLA--VKSNIITNGLRYSLATGnwgdqkrsmvnrvGVSQVLNRYTFASTLSH 480
Cdd:COG0085 325 RVGLSRMERVV-RErM----TTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTH 386
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 481 LRRTNT----PIGRDgklaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSvgspsapiiEFleewgletl 552
Cdd:COG0085 387 KRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY--------- 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 553 edynpsaspnatkvfvngvwlgvhrdpahltetlrslrrrldisaevsivrdirekelrlftdaGRICRPLFIVDNNpns 632
Cdd:COG0085 445 ----------------------------------------------------------------GFIETPYRKVENG--- 457
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 633 errgelcirkehiqqLIEDKdrydidpeqrfgwtalvssglIEYLDAEEEETVMIAMSPEDLEASrqmqaGYEVKEELDP 712
Cdd:COG0085 458 ---------------KVTDE---------------------IEYLTADEEENYYIAQANAPLDED-----GNFLEERVLV 496
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 713 AQRVKP---APNPHvhawTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQvrmdtmanILYYP- 788
Cdd:COG0085 497 RYRGEEvlvPPEEV----DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPl 564
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 789 -------------QKPLAttRSMEYLK------------FRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSI 843
Cdd:COG0085 565 qkfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSI 642
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 844 FYRTYTDQEK--KIGMtvmEE--FERPVRSTTLrmkhgtYDKLEDDGLIAPGTRVSGEDIIIGKTAP---IPLDHEELGQ 916
Cdd:COG0085 643 HIEEYEIEARdtKLGP---EEitRDIPNVSEEA------LRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTPEERLL 713
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 917 RTQLHAK----RDVSTPLRSTESGIVDQVMVTTNQEG-------LKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRH 985
Cdd:COG0085 714 RAIFGEKarevRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQ 793
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 986 EDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGH 1065
Cdd:COG0085 794 EDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGR 873
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSD 1145
Cdd:COG0085 874 TGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD 953
|
1210 1220 1230 1240 1250 1260
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 63054498 1146 ayrvivcDICGLIAIasykkdsYEcrSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLFTKN 1208
Cdd:COG0085 954 -------DVCGRVKV-------YE--AIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
30-441 |
0e+00 |
|
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 569.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 30 LARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDvtrRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNL 109
Cdd:pfam04563 2 LVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGD---KLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 110 TYSSPLYVDMRKKVMVAADSnvpigeeewlveeedeEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFI 189
Cdd:pfam04563 79 TYSAPLYVDLELSVYNGEDI----------------KPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFI 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 190 INGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMarnTENSGQTIRATLPYIRSDIPIV 269
Cdd:pfam04563 143 INGSEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVL---EYLSNGTIYFKFPYIKKEIPIV 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 270 IVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVI--QDKDIALDYIGKRGST---TGVTREKRLRYAHDILQK 344
Cdd:pfam04563 220 IILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEILQK 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 345 ELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVET 424
Cdd:pfam04563 300 EVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGS 379
|
410
....*....|....*..
gi 63054498 425 NREFNLTLAVKSNIITN 441
Cdd:pfam04563 380 PDDLMLQLLVNAKPITS 396
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
18-1204 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1275.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 18 WTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDdstltldqyaqhTGAQGDVTRRYEINFGQIYLSRPTMTEADGSTT 97
Cdd:PRK08565 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE------------FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSER 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 98 TMFPQEARLRNLTYSSPLYVDMRkkvmVAADSnvpigeeewlveeEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDL 177
Cdd:PRK08565 70 PITPMEARLRNLTYAAPLYLTMI----PVENG-------------IEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEI 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 178 NECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSAlERGSRLISSMQIKlmarnteNSGqTIRA 257
Cdd:PRK08565 133 GEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISS-RAGYRAQVTVERR-------KDG-TIYV 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 258 TLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPndfQMLEMMKPCIEEAF-VIQDKDIALDYIGKRgSTTGVTREKRLR 336
Cdd:PRK08565 204 SFPAVPGKIPFVILMRALGLETDRDIVYAVSLDP---EIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIE 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 337 YAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYK 416
Cdd:PRK08565 280 RAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKY 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 417 YMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDqkrsmvNRVGVSQVLNRYTFASTLSHLRRTNTPIGRDGKLAK 496
Cdd:PRK08565 360 QLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVG------GRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFE 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 497 PRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVH 576
Cdd:PRK08565 434 ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYH 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 577 RDPAHLTETLRSLRRRLDISAEVSI--VRDIREKELRLFTDAGRICRPLFIVDNnpnserrGELCIRKEHIQQLiedkDR 654
Cdd:PRK08565 514 PDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKL----KK 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 655 YDIDpeqrfgWTALVSSGLIEYLDAEEEETVMIAMSPEDLeasrqmqagyeVKEeldpaqrvkpapnphvHawTHCEIHP 734
Cdd:PRK08565 583 GELT------FDDLVKMGVIEYLDAEEEENAYVALDPEDL-----------TPE----------------H--THLEIWP 627
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 735 AMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIV 814
Cdd:PRK08565 628 PAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVV 707
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 815 AILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPvrSTTLRMKHG--TYDKLEDDGLIAPGT 892
Cdd:PRK08565 708 AVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEV 785
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 893 RVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASR 972
Cdd:PRK08565 786 EVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASR 865
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 973 HGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHG 1052
Cdd:PRK08565 866 HGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLG 945
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1053 FQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGC 1132
Cdd:PRK08565 946 YKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGA 1025
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 63054498 1133 SSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRL 1204
Cdd:PRK08565 1026 AMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRL 1097
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
30-1205 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 1180.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 30 LARQQLFSFDEFVQNTMQEIVDDDSTLTLDqyaqhtgaqgDVTRRYEINFGQIYLSRPTMTEaDGSTTTMFPQEARLRNL 109
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDT----------DDDGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 110 TYSSPLYVDMRKKVMvaadsnvpigeeewlvEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFI 189
Cdd:cd00653 70 TYSAPLYVDIRLTVN----------------DKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFI 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 190 INGSEKVIIAQERSAANIVQVFkkaaPSPIAYVAEIRSALERGSRLISSMQIKLMARNtensgQTIRATLPYIRsdipiv 269
Cdd:cd00653 134 INGTEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK-----DRIYVRIDLKR------ 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 270 ivfralgvvpdrdilehicydpndfqmlemmkpcieeafviqdKDIALDYIGKRGsttgvtrekrlryahdilqkellph 349
Cdd:cd00653 199 -------------------------------------------QEEALKYIGKRF------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 350 ittmegfetrkaFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREFN 429
Cdd:cd00653 211 ------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT 278
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 430 LTLAVKSNIITNGLRYSLATGNWGDqKRSMVNRVGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGMV 508
Cdd:cd00653 279 PQLLINSKPITSGIKEFLATGNWGS-KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRI 357
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 509 CPAETPEGQACGLVKNLSLMSYVSvgspsapiiefleewgletledynpsaspnatkvfvngvwlgvhrdpahltetlrs 588
Cdd:cd00653 358 CPIETPEGENCGLVKNLALMARIS-------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 589 lrrrldisaevsivrdirekelrlftdaGRICRPLFIVDNNpnserrgelcirkehiqqliedkdrydidpeqrfgwtal 668
Cdd:cd00653 382 ----------------------------GRIERPYRIVEKE--------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 669 vssglieyldaeeeetvmiamspedleasrqmqagyevkeeldpaqrvkpapnphvhaWTHCEIHPAMILGILASIIPFP 748
Cdd:cd00653 395 ----------------------------------------------------------VTHIEISPSQILSVAASLIPFP 416
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 749 DHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSI 828
Cdd:cd00653 417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 829 IMNQASIDRGLFRSIFYRTYTDQEKKIGMTvmeeFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIP 908
Cdd:cd00653 497 IINKSSVDRGFFRSIHYKKYEIELRKTKNG----PEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 909 LDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTT---NQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRH 985
Cdd:cd00653 573 ETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQ 652
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 986 EDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGH 1065
Cdd:cd00653 653 EDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGR 732
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSD 1145
Cdd:cd00653 733 TGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSD 812
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1146 AYRVIVCDICGLIAIASYkkdsyeCRSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLF 1205
Cdd:cd00653 813 DVVARVCVKCGIILSANL------CRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
566-1204 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 769.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 566 VFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNnpnserrGELCIRKEHI 645
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 646 QQLiedkdrydidPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLeasrqmqagyevkeeldpaqrvkpAPNphvH 725
Cdd:TIGR03670 74 EKL----------KEGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL------------------------TPE---H 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 726 awTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRE 805
Cdd:TIGR03670 117 --THLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDD 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 806 LPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPvrSTTLRMKHG--TYDKLE 883
Cdd:TIGR03670 195 RPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGeeAYKHLD 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 884 DDGLIAPGTRVSGEDIIIGKTAPiPL---DHEELGQRTQlhAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRST 960
Cdd:TIGR03670 273 EDGIVYPEVEVKGGDVLIGKTSP-PRfleELREFGLVTE--RRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDL 349
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 961 RIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVT 1040
Cdd:TIGR03670 350 RIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEP 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1041 VEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFG 1120
Cdd:TIGR03670 430 EEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFG 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1121 EMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI 1200
Cdd:TIGR03670 510 EMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGI 589
|
....
gi 63054498 1201 APRL 1204
Cdd:TIGR03670 590 SPRL 593
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
564-1204 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 730.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 564 TKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNnpnserrGELCIRKE 643
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 644 HIQQLiedkDRYDIDpeqrfgWTALVSSGLIEYLDAEEEETVMIAMSPEDLEasrqmqagyevkEEldpaqrvkpapnph 723
Cdd:PRK07225 78 HIEKL----KNGELT------FDDLVKQGVIEYLDAEEEENAYIAVYEEDLT------------EE-------------- 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 724 vHawTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKF 803
Cdd:PRK07225 122 -H--THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGF 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 804 RELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPvrSTTLRMKHG--TYDK 881
Cdd:PRK07225 199 DERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIP--DKDVRGYRGeeAYRH 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 882 LEDDGLIAPGTRVSGEDIIIGKTAPiPL---DHEELGQRTQlhAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMR 958
Cdd:PRK07225 277 LDEDGLVNPETEVKEGDVLIGKTSP-PRfleEPDDFGISPE--KRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVR 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 959 STRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTD 1038
Cdd:PRK07225 354 DLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSG 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1039 VTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLR 1118
Cdd:PRK07225 434 EDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLR 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1119 FGEMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSM 1198
Cdd:PRK07225 514 FGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSL 593
|
....*.
gi 63054498 1199 NIAPRL 1204
Cdd:PRK07225 594 GIAPRL 599
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
21-1208 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 719.58 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 21 ISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTldqyaqhtgaqgDVTRRYEINFGQIYLSRPTMTeadgstttmf 100
Cdd:COG0085 7 IKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE------------DFTGNLSLEFGDYRLGEPKYT---------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 101 PQEARLRNLTYSSPLYVDMRkkvmVAADSNVPIgeeewlveeedeEPSKVFIGKIPIMLRStfcilngvsdselydlnec 180
Cdd:COG0085 65 PEECKERDLTYAAPLYVKVR----LVNKETGEI------------KEQEVFMGDFPLMTDS------------------- 109
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 181 pydqgGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSAleRGSRLIssmqIKLMARNTensgqtIRATLP 260
Cdd:COG0085 110 -----GTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLE----FETDKDGT------IYVRID 172
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 261 YIRsDIPIVIVFRALGVVPDRDILEHICYDPNDfqmlEMMKPCIEEAfVIQDKDIALDYIGKR---GSTtgVTREKRLRY 337
Cdd:COG0085 173 RKR-KIPVTVLLRALGLETDEEILEAFGDDPIQ----EYILATLEKD-NTKTQEEALLEIYRKlrpGEP--PTIERAEQL 244
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 338 AHDILQKEL---LPHI---------TTMEGFETR--KAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLF 403
Cdd:COG0085 245 LDNLFFDPKrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQF 324
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 404 RMLFRKMTRDVyKY-MqkcvETNREFNLTLA--VKSNIITNGLRYSLATGnwgdqkrsmvnrvGVSQVLNRYTFASTLSH 480
Cdd:COG0085 325 RVGLSRMERVV-RErM----TTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTH 386
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 481 LRRTNT----PIGRDgklaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSvgspsapiiEFleewgletl 552
Cdd:COG0085 387 KRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY--------- 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 553 edynpsaspnatkvfvngvwlgvhrdpahltetlrslrrrldisaevsivrdirekelrlftdaGRICRPLFIVDNNpns 632
Cdd:COG0085 445 ----------------------------------------------------------------GFIETPYRKVENG--- 457
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 633 errgelcirkehiqqLIEDKdrydidpeqrfgwtalvssglIEYLDAEEEETVMIAMSPEDLEASrqmqaGYEVKEELDP 712
Cdd:COG0085 458 ---------------KVTDE---------------------IEYLTADEEENYYIAQANAPLDED-----GNFLEERVLV 496
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 713 AQRVKP---APNPHvhawTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQvrmdtmanILYYP- 788
Cdd:COG0085 497 RYRGEEvlvPPEEV----DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPl 564
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 789 -------------QKPLAttRSMEYLK------------FRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSI 843
Cdd:COG0085 565 qkfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSI 642
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 844 FYRTYTDQEK--KIGMtvmEE--FERPVRSTTLrmkhgtYDKLEDDGLIAPGTRVSGEDIIIGKTAP---IPLDHEELGQ 916
Cdd:COG0085 643 HIEEYEIEARdtKLGP---EEitRDIPNVSEEA------LRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTPEERLL 713
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 917 RTQLHAK----RDVSTPLRSTESGIVDQVMVTTNQEG-------LKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRH 985
Cdd:COG0085 714 RAIFGEKarevRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQ 793
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 986 EDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGH 1065
Cdd:COG0085 794 EDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGR 873
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSD 1145
Cdd:COG0085 874 TGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD 953
|
1210 1220 1230 1240 1250 1260
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 63054498 1146 ayrvivcDICGLIAIasykkdsYEcrSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLFTKN 1208
Cdd:COG0085 954 -------DVCGRVKV-------YE--AIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
30-441 |
0e+00 |
|
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 569.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 30 LARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDvtrRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNL 109
Cdd:pfam04563 2 LVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGD---KLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 110 TYSSPLYVDMRKKVMVAADSnvpigeeewlveeedeEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFI 189
Cdd:pfam04563 79 TYSAPLYVDLELSVYNGEDI----------------KPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFI 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 190 INGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMarnTENSGQTIRATLPYIRSDIPIV 269
Cdd:pfam04563 143 INGSEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVL---EYLSNGTIYFKFPYIKKEIPIV 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 270 IVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVI--QDKDIALDYIGKRGST---TGVTREKRLRYAHDILQK 344
Cdd:pfam04563 220 IILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEILQK 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 345 ELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVET 424
Cdd:pfam04563 300 EVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGS 379
|
410
....*....|....*..
gi 63054498 425 NREFNLTLAVKSNIITN 441
Cdd:pfam04563 380 PDDLMLQLLVNAKPITS 396
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
741-1113 |
0e+00 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 541.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 741 LASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 820
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 821 GYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTvmEEFERPVrsttLRMKHGTYDKLEDDGLIAPGTRVSGEDII 900
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPI--EEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 901 IGKTAPIPLD---HEELGQRTQLhaKRDVSTPLRSTESGIVDQVMV-TTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQK 976
Cdd:pfam00562 155 VGKVGPTELTkllRAIFGEKARD--VKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 977 GTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFT--DVTVEAVSKLLRSHGFQ 1054
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYN 312
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 63054498 1055 SRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSR 1113
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
13-552 |
1.08e-132 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 414.35 E-value: 1.08e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 13 TQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDqyaqhtgaqgdVTRRYEINFGQIYLSRPTMTEA 92
Cdd:PRK09606 1 MMEDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETE-----------IEDGVYVELGKIRVGKPVVKEA 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 93 DGSTTTMFPQEARLRNLTYSSPLYVDMrkkVMVAADSNVPigeeewlveeedeePSKVFIGKIPIMLRSTFCILNGVSDS 172
Cdd:PRK09606 70 DGSEREIYPMEARLRNLTYSAPLYLEM---SPVEGGEEEE--------------PEEVYIGELPVMVGSKICNLYGLSEE 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 173 ELYDLNECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSAlERGSR-LIssmqikLMARNTENs 251
Cdd:PRK09606 133 ELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKILVEKDERYGDRIEVAKVFSQ-RRGYRaLV------TVERNRDG- 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 252 gqTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNdFQMLemMKPCIEEAfVIQDKDIALDYIGKRGSTtGVTR 331
Cdd:PRK09606 205 --LLEVSFPSVPGSIPFVILMRALGLETDEEIVEAVSDDPE-IVKF--MLENLEEA-EVDTQEEALEYIGKRVAP-GQTK 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 332 EKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMT 411
Cdd:PRK09606 278 EYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLA 357
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 412 RDVyKY-MQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWgdqkrsMVNRVGVSQVLNRYTFASTLSHLRRTNTPIGR 490
Cdd:PRK09606 358 RDV-KYqLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSR 430
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 63054498 491 DGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETL 552
Cdd:PRK09606 431 SQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
21-1151 |
2.35e-69 |
|
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 273928 [Multi-domain] Cd Length: 1065 Bit Score: 253.43 E-value: 2.35e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 21 ISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLtlDQYAQHTGAQGDVTRRYEINFGQIYLSRPTMTeadgstttmf 100
Cdd:TIGR02013 11 IPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGL--EEVFKSIFPIEDYTGNIELEYLSYRLGEPKYS---------- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 101 PQEARLRNLTYSSPLYVDMRKKVMVAADSNvpigeeewlveeeDEEPSKVFIGKIPIMlrstfcilngvSDSelydlnec 180
Cdd:TIGR02013 79 VEECKERGLTYSAPLKVKLRLINKEEDGTK-------------EIKEQDVYMGDIPLM-----------TDR-------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 181 pydqgGYFIINGSEKVIIAQ-ERSAAnivQVFKKAAPSP----IAYVAEIRSalERGSRLISSMQIKlmarntensgqti 255
Cdd:TIGR02013 127 -----GTFIINGAERVVVSQlHRSPG---VFFSSEKDTTksgkVLFSARIIP--YRGSWLEFETDKK------------- 183
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 256 raTLPYIRSD----IPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAfviqdkdiALDYIGKR-----GST 326
Cdd:TIGR02013 184 --DVLYVRIDrkrkLPATVLLRALGYTIDTLILNRLGSGEYIRNTLRKDPTNSEEE--------ALVEIYRKlrpgePPT 253
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 327 TGVTRE--KRL-----RYahDI-------LQKELLPHITTMEGFETrKAFFLGYMIHRMLLCAlERREPDDRDHFGKKRL 392
Cdd:TIGR02013 254 VEAARSllENLffdpkRY--DLgrvgrykLNKKLGLDVPESIGVLT-KEDIIATIKYLIKLRN-GKGEIDDIDHLGNRRI 329
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 393 DLAGPLLASLFRMLFRKMTRDVYKYMqkcveTNREFNlTLAVKSNIITNGLRYSLatgnwgdqkRSMVNRVGVSQVLNRY 472
Cdd:TIGR02013 330 RSVGELLQNQFRVGLARMERIVRERM-----STQDTD-TLTPQDLINAKPISAAI---------KEFFGSSQLSQFMDQT 394
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 473 TFASTLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSlmSYvsvgspsapiiefleewg 548
Cdd:TIGR02013 395 NPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLS--TY------------------ 454
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 549 letledynpsaspnatkvfvngvwlgvhrdpahltetlrslrrrldisAEVSivrdirekelrlftDAGRICRPLFIVDN 628
Cdd:TIGR02013 455 ------------------------------------------------ARVN--------------EYGFIETPYRKVKD 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 629 NpnserrgelcirkehiqqliedkdryDIDPEQRfgwtalvssglIEYLDAEEEETVMIA-----MSPEDLEASRQMQAG 703
Cdd:TIGR02013 473 G--------------------------KVVVTDE-----------IDYLTADEEDNYVIAqanapLDENGRFVEDLVVAR 515
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 704 YEVKEELDPAQRVkpapnphvhawTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAM---------------- 767
Cdd:TIGR02013 516 YRGEITLVSPDQV-----------DYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmea 584
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 768 ---------------GV--YLTNYQVR-------MDTMANILYYP--------------QKP-------------LATTR 796
Cdd:TIGR02013 585 kvardsgavivakrgGVveYVDAKRIVirydedeEEPDGGIDIYRllkyqrsnqdtcinQRPivsvgdrveagdvLADGP 664
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 797 SMEylkFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFyrtytdqekkigmtvMEEFERPVRSTTLRMKH 876
Cdd:TIGR02013 665 STD---LGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIH---------------IEEYEVEARDTKLGPEE 726
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 877 GTYD----------KLEDDGLIAPGTRVSGEDIIIGKTAP---IPLDHEELGQRTQLHAK----RDVSTPLRSTESGIVD 939
Cdd:TIGR02013 727 ITRDipnvseealrNLDENGIVRIGAEVKAGDILVGKVTPkgeTELTPEEKLLRAIFGEKardvRDTSLRVPPGVEGTVI 806
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 940 QVMVTTNQEG-------LKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTV 1012
Cdd:TIGR02013 807 DVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNI 886
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1013 AHLVECQLSKVSALSGFEGD--ATP-FTDVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVD 1089
Cdd:TIGR02013 887 GQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVD 966
|
1210 1220 1230 1240 1250 1260
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 63054498 1090 DKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSD-------AYRVIV 1151
Cdd:TIGR02013 967 DKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvvgrtkAYEAIV 1035
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
204-393 |
2.16e-58 |
|
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 199.11 E-value: 2.16e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 204 AANIVQVFKKAAPSPIAYVAEIRSALERGSRLissmqiklmarNTENSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDI 283
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGSWL-----------KLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREI 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 284 LEHICYDPNDFQMLEMMKPCIEEAFVIQDKDIALDYIGKrGSTTGVTREKRLRYAHDILQK-----ELLPHITTMEGFET 358
Cdd:pfam04561 70 LDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEPFEN 148
|
170 180 190
....*....|....*....|....*....|....*..
gi 63054498 359 R--KAFFLGYMIHRMLLCALERREPDDRDHFGKKRLD 393
Cdd:pfam04561 149 ErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
154-1145 |
6.55e-54 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 205.71 E-value: 6.55e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 154 KIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIAQersaanIVQvfkkaapSPIAYvaeIRSALERGS 233
Cdd:CHL00207 74 QIYLPLKFINLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQ------IIR-------SPGIY---FKKEIKKNS 137
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 234 RLISSMQIKLmarnteNSGQTIRATLP-----YIRSD----IPIVIVFRALGVvPDRDILEHICYDPN------------ 292
Cdd:CHL00207 138 NKIYSATLIP------NRGSWIKFELDknkeiWIRIDknrkKPLIIFLKALGL-TDQDIYSRLTKSEFlkklkpillnsn 210
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 293 -------DFQMLEMMKPcIEEAFVIQDKDIALDYI-GKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFetrkaFFL 364
Cdd:CHL00207 211 sytneeiLLEIYKNLSP-IEPATVNDANQNLFSRFfDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDIL-----SII 284
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 365 GYMIHrmlLCaLERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVetnrefnLTLAVKSNIITNGLR 444
Cdd:CHL00207 285 DKLIN---LK-INKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICD-------IDSLSKFNLINPKPL 353
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 445 YSLATGNWGdqkrsmVNRVgvSQVLNRYTFASTLSHLRRTNT--PIGRDgKLAKP---RQLHNTHWGMVCPAETPEGQAC 519
Cdd:CHL00207 354 IALIREFFG------SSQL--SQYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNC 424
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 520 GLVKnlSLMSYVSVgspsapiieflEEWGLetLEDYNPSASPNATKVFVNgvwlgvhrdPAHLTETLRSLRRRL--DISa 597
Cdd:CHL00207 425 GLIG--SLATNARI-----------NKFGF--IETPFYKVINGKVKKFGN---------PIYLTADSEDLYRIApnDIN- 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 598 evsivrdIREKElrlftdagricrplFIVDNNPNSERRGELCIRKehiqqlIEDKDRYDIDPEQRFGWTALvssgLIEYL 677
Cdd:CHL00207 480 -------LNKNN--------------YFKKNIIPVRYKQEFKTVN------PSKVDFIAISPIQVFSIAES----LIPFL 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 678 DAEEEETVMIAmspedleASRQMQA-------------GYEVKEELDPAQRVKPAPNPHVHAWTHCEIHpamilgILasi 744
Cdd:CHL00207 529 EHNDANRALMG-------SNMQRQAvpllypekpivgtGYEKQIALDSGMTIISLTEGIVVSVSAYKII------IQ--- 592
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 745 ipfpdHNQSPRNTYqsamgkqamgvYLTNYQV-RMDTMANilyypQKP-------------LATTRSMeylKFRELPAGQ 810
Cdd:CHL00207 593 -----DDNNRYIHY-----------YLQKYQRsNQNTCIN-----YRPivwvgekinigqiLADGSDI---DNSELALGQ 648
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 811 NAIVAILCYSGYNQEDSIIMNQASIDRGLFRSI---FYRTYTDQEKKigmtVMEEFERPVRSTTLRMKHgtydKLEDDGL 887
Cdd:CHL00207 649 NVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIhieKYEIELRQTKL----GSEEITRNIPNVSEYSLK----NLDENGI 720
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 888 IAPGTRVSGEDIIIGKTAPIPlDHEELGQRTQLHA-----KRDV-STPLRST--ESGIVDQVMVTTNQEGLKF------- 952
Cdd:CHL00207 721 ISIGSKVLAGDILVGKITPKG-ESDQLPEGKLLRAifgekAKDVkDTSLRMPngGYGRVIKVEIFSRSKGDELkfgyylk 799
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 953 VKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLskvsALSGFEGD 1032
Cdd:CHL00207 800 IRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLL----GLAGDNLN 875
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1033 A----TPFTDVTVEAVSKLLRSHGFQSRGFE---------------VMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIH 1093
Cdd:CHL00207 876 KrfkiLPFDEMYGSEYSRILINNKLNQASIKnneywlfnsyhpgkmVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIH 955
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|..
gi 63054498 1094 ARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSD 1145
Cdd:CHL00207 956 ARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD 1007
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
34-1123 |
3.45e-49 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 191.08 E-value: 3.45e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 34 QLFSFDEFVQNT-------MQEIVDDDSTLTldqyaqhtgaqgDVTRRYEINFGQIYLSRPTMTEadgstttmfpQEARL 106
Cdd:PRK00405 31 QLDSFDWFLQLDvppedegLEEVFRSIFPIE------------DFNGNLSLEFVSYELGEPKYDV----------EECKE 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 107 RNLTYSSPLYVDMRKkvmvaadSNVPIGEEEWlveeedeepSKVFIGKIPIMlrsTfcilngvsdselydlnecpydQGG 186
Cdd:PRK00405 89 RGLTYSAPLRVKLRL-------INKETGEIKE---------QEVYMGDIPLM---T---------------------ENG 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 187 YFIINGSEKVIIAQ-ERSAAnivqVF-----KKAAPSPIAYVAEIRSAleRGSRLissmQIKLMARNTensgqtiratlP 260
Cdd:PRK00405 129 TFIINGTERVIVSQlHRSPG----VYfdhdkDKTSSGKLLYSARIIPY--RGSWL----EFEFDPKDI-----------L 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 261 YIRSD----IPIVIVFRALGVVpDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQDKDIALDYIGKRGSTTGVTREKRLR 336
Cdd:PRK00405 188 YVRIDrrrkLPVTVLLRALGYS-DEEILDLFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGP 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 337 YAHDILQKEllPHITTMEGF---------------ETRKAFF-----------LG----YMIHRML-------------- 372
Cdd:PRK00405 267 YIRNTLEKD--PTSSREEALveiyrrlrpgepptvEAARSLLenlffdpkrydLSkvgrYKLNKKLgldededvrvltke 344
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 373 --------LCALE--RREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMqkcveTNREFNlTLAVKS--NI-- 438
Cdd:PRK00405 345 diiatikyLINLRngKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM-----SLQDLD-TLTPQDliNAkp 418
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 439 ITNGLRYSLATGnwgdQkrsmvnrvgVSQvlnrytF------ASTLSHLRRTNT--PIG----------RDgklakprqL 500
Cdd:PRK00405 419 VVAAIKEFFGSS----Q---------LSQ------FmdqtnpLSELTHKRRLSAlgPGGltreragfevRD--------V 471
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 501 HNTHWGMVCPAETPEGQACGLVKNLSlmSYVSVgspsapiieflEEWG-LETledynpsaspnatkvfvngvwlgvhrdp 579
Cdd:PRK00405 472 HPTHYGRICPIETPEGPNIGLINSLA--TYARV-----------NEYGfIET---------------------------- 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 580 ahltetlrslrrrldisaevsivrdirekelrlftdagricrPLFIVDNNpnserrgelcirkehiqqLIEDKdrydidp 659
Cdd:PRK00405 511 ------------------------------------------PYRKVVDG------------------KVTDE------- 523
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 660 eqrfgwtalvssglIEYLDAEEEETVMIAmspedleasrqmQAGYEVKEE-----------------LDPAQRVkpapnp 722
Cdd:PRK00405 524 --------------IVYLTADEEDNYVIA------------QANAPLDEDgrfvdelvtarykgefvLVPPEEV------ 571
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 723 hvhawTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAmgVYLTN-----------YQVRMDTMANIL------ 785
Cdd:PRK00405 572 -----DYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQA--VPLLRpeaplvgtgmeRRVARDSGAVVVakrdgv 644
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 786 -----------YYPQKPLATTRSMEY--LKFR-----------------------------------ELPAGQNAIVAIL 817
Cdd:PRK00405 645 veyvdasrivvRVEELDPGEDGVDIYnlIKFQrsnqntcinqrpivkvgdrvekgdvladgpstdngELALGQNVLVAFM 724
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 818 CYSGYNQEDSIIMNQASIDRGLFRSIfyrtytdqekKIgmtvmEEFERPVRSTtlrmKHG----TYD----------KLE 883
Cdd:PRK00405 725 PWNGYNFEDAILISERLVKEDVFTSI----------HI-----EEYEIEARDT----KLGpeeiTRDipnvseealrNLD 785
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 884 DDGLIAPGTRVSGEDIIIGKTAP---IPLDHEE-LgqrtqLHA----K-RDV-STPLR--STESGIVDQVMV-TTNQEG- 949
Cdd:PRK00405 786 ESGIVRIGAEVKPGDILVGKVTPkgeTELTPEEkL-----LRAifgeKaRDVkDTSLRvpHGEEGTVIDVKVfTRIEQGd 860
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 950 ------LKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKV 1023
Cdd:PRK00405 861 elppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWA 940
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1024 SALSG--FegdATP-FTDVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPV 1100
Cdd:PRK00405 941 AKGLGikF---ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPY 1017
|
1290 1300
....*....|....*....|...
gi 63054498 1101 QILTRQPVEGRSRDGGLRFGEME 1123
Cdd:PRK00405 1018 SLVTQQPLGGKAQFGGQRFGEME 1040
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1115-1207 |
6.55e-41 |
|
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 145.04 E-value: 6.55e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1115 GGLRFGEMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYkkdsyeCRSCQNRTRFSQVYLPYAAKLLFQE 1194
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNK------CPICKGETDISPGYIPESFKLLFQE 74
|
90
....*....|...
gi 63054498 1195 LMSMNIAPRLFTK 1207
Cdd:pfam04560 75 LQSLGIDPRLLLE 87
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
382-1150 |
4.57e-38 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 156.24 E-value: 4.57e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 382 DDRDHFGKKRLDLAGPLLAS-----LFRMlfRKMTRDVYKYMQKCVETNREFNLtlaVKSNIITNGLRYSLATGNwgdqk 456
Cdd:PRK09603 455 DDRDHLGNRRIRAVGELLANelhsgLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTIMEFFMGGQ----- 524
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 457 rsmvnrvgVSQVLNRYTFASTLSHLRRTNTpIGrDGKLAK------PRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSY 530
Cdd:PRK09603 525 --------LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLSTFTR 594
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 531 VS-VGSPSAPIIEFLEewgletledynpsaspnaTKVFVNGVWLGVHRDPAHLTETLRSLrrrldISAEVSIVRDIREke 609
Cdd:PRK09603 595 VNdLGFIEAPYKKVVD------------------GKVVGETIYLTAIQEDSHIIAPASTP-----IDEEGNILGDLIE-- 649
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 610 lrlftdagricrplfivdnnpnSERRGELCIRKEHIQQLIedkdryDIDPEQRFGwtalVSSGLIEYLDAEEEETVMIAm 689
Cdd:PRK09603 650 ----------------------TRVEGEIVLNEKSKVTLM------DLSSSMLVG----VAASLIPFLEHDDANRALMG- 696
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 690 spedleASRQMQAgyevKEELDPAQRVKPAPNPHVHAWTHCEIHPAMILGILASIipfpdhnqSPRNTYqsAMGKQAMGV 769
Cdd:PRK09603 697 ------TNMQRQA----VPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKI--------DSKNIY--ILGEGKEEA 756
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 770 YLTNYQVRMDTMANI-LYYPQKPL-------------ATTRSMEYlkfRELPAGQNAIVAILCYSGYNQEDSIIMNQASI 835
Cdd:PRK09603 757 YIDAYSLQKNLRTNQnTSFNQVPIvkvgdkveagqiiADGPSMDR---GELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 836 DRGLFRS--IFYRTYTDQEKKIGMtvmEEFERPVRSTtlrmKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAP------- 906
Cdd:PRK09603 834 KDDIFTSthIYEKEVDARELKHGV---EEFTADIPDV----KEEALAHLDESGIVKVGTYVSAGMILVGKTSPkgeikst 906
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 907 --------------------------------------------------------------------IPLDHEELGQRT 918
Cdd:PRK09603 907 peerllraifgdkaghvvnkslycppslegtvidvkvftkkgyekdarvlsayeeekakldmehfdrlTMLNREELLRVS 986
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 919 QLHAK-----------------------------------------RDVSTPLRSTESGIVDQ--VMVTTNQEGL----- 950
Cdd:PRK09603 987 SLLSQaileepfshngkdykegdqipkeeiasinrftlaslvkkysKEVQNHYEITKNNFLEQkkVLGEEHEEKLsilek 1066
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 951 ---------KFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLS 1021
Cdd:PRK09603 1067 ddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLG 1146
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1022 KV--------------------------------------------------SALSGFEGD-------ATP-FTDVTVEA 1043
Cdd:PRK09603 1147 LVgkefgkqiasmledktkdfakelrakmleianainekdpltihalencsdEELLEYAKDwskgvkmAIPvFEGISQEK 1226
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1044 VSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEME 1123
Cdd:PRK09603 1227 FYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEME 1306
|
970 980 990
....*....|....*....|....*....|....
gi 63054498 1124 RDCQISHGCSSVLRERLFDCSD-------AYRVI 1150
Cdd:PRK09603 1307 VWALEAYGAAHTLKEMLTIKSDdirgrenAYRAI 1340
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
79-1123 |
5.70e-35 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 145.43 E-value: 5.70e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 79 FGQIY-LSRPTMTEadgstttmfpQEARLRNLTYSSPLYVdmrkkvmvaadsnvPIGEEEWLVEEEDEEPskVFIGKIPI 157
Cdd:CHL00001 53 FVETYqLVEPLIKE----------RDAVYESLTYSSELYV--------------PAGLIWKKSRDMQEQT--VFIGNIPL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 158 MlrstfcilngvsdselydlnecpyDQGGYFIINGSEKVIIAQersaanIVQvfkkaapSP-IAYVAEI----RSAL--- 229
Cdd:CHL00001 107 M------------------------NSLGTFIINGIYRVVINQ------ILR-------SPgIYYRSELdhngISVYtgt 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 230 ---ERGSRLissmqiKLmarntensgQTIRATLPYIRSD----IPIVIVFRALGVvPDRDILEHICYdPNDFQ------- 295
Cdd:CHL00001 150 iisDWGGRL------EL---------EIDRKARIWARVSrkqkISILVLLSAMGL-NLREILDNVCY-PEIFLsflndke 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 296 ----------MLEMMK--PCIEEAFVIQD---KDIALDYIGKRGSTTGVTRE---KRLRYahDILQKE--LLPH-ITTME 354
Cdd:CHL00001 213 kkkigskenaILEFYQqfACVGGDPVFSEslcKELQKKFFQQRCELGRIGRRnmnRKLNL--DIPENNtfLLPQdVLAAA 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 355 GFETRKAFFLGymihrmllcalerrEPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREFNLTLAV 434
Cdd:CHL00001 291 DYLIGMKFGMG--------------TLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLV 356
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 435 KSNIITNGLR-----YSLatgnwgdqkrsmvnrvgvSQVLNRYTFASTLSHLRRTNT--PIGRDGKLA--KPRQLHNTHW 505
Cdd:CHL00001 357 TSTPLTTTYEsffgsHPL------------------SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHY 418
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 506 GMVCPAETPEGQACGLVKnlSLMSYVSVGSpsapiiefleeWG-LETledynpsaspnatkvfvngvwlgvhrdpahlte 584
Cdd:CHL00001 419 GRICPIDTSEGINAGLIG--SLAIHARIGH-----------WGsLES--------------------------------- 452
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 585 tlrslrrrldisaevsivrdirekelrlftdagricrPLFIVDNNPNSERrgelcirkehiqqliedkdrydidpeqrfg 664
Cdd:CHL00001 453 -------------------------------------PFYEISERSKEER------------------------------ 465
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 665 wtalvssglIEYLDAEEEETVMIAmSPEDLEASRQMQagyevKEELDPAQR----VKPAPNpHVHAWThceIHPAMILGI 740
Cdd:CHL00001 466 ---------MVYLSPSEDEYYMIA-AGNSLALNQGIQ-----EEQVVPARYrqefLTIAWE-QIHLRS---IFPFQYFSI 526
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 741 LASIIPFPDHNQSPRNTYQSAMGKQA---------------------------------------------------MGV 769
Cdd:CHL00001 527 GASLIPFLEHNDANRALMGSNMQRQAvplsrsekcivgtglerqvaldsgvvaiaehegkiiytdtdkiilsgngdtLSI 606
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 770 YLTNYQvR--MDTMANilyypQKPlaTTRSMEYLKFRELPA------------GQNAIVAILCYSGYNQEDSIIMNQASI 835
Cdd:CHL00001 607 PLVMYQ-RsnKNTCMH-----QKP--QVRRGKCVKKGQILAdgaatvggelalGKNVLVAYMPWEGYNFEDAVLISERLV 678
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 836 DRGLFRSIFYRTYtdqEKKIGMTvMEEFERPVR------STTLRmkhgtydKLEDDGLIAPGTRVSGEDIIIGKTAPipL 909
Cdd:CHL00001 679 YEDIYTSFHIRKY---EIQTHVT-SQGPERITKeiphleAHLLR-------NLDKNGIVMLGSWVETGDILVGKLTP--Q 745
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 910 DHEELGQRTQLHAKRDVS---------TPLRSTESG---IVDQVMVT---TNQEGLKFVKVRMRSTRIPQIGDKFASRHG 974
Cdd:CHL00001 746 EAEESSYAPEGRLLRAIFgiqvstskeTCLKLPIGGrgrVIDVRWIQkkgGSSYNPETIHVYILQKREIQVGDKVAGRHG 825
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 975 QKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLskvsalsGFEGD-------ATPFTD-VTVEAVSK 1046
Cdd:CHL00001 826 NKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL-------GLAGDllnrhyrIAPFDErYEQEASRK 898
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1047 LLRSHGFQSRG-------FEVMY-------HGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRS 1112
Cdd:CHL00001 899 LVFSELYEASKqtanpwvFEPEYpgksrlfDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRS 978
|
1210
....*....|.
gi 63054498 1113 RDGGLRFGEME 1123
Cdd:CHL00001 979 KQGGQRVGEME 989
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
566-627 |
5.06e-33 |
|
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pssm-ID: 428012 [Multi-domain] Cd Length: 62 Bit Score: 121.70 E-value: 5.06e-33
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 63054498 566 VFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVD 627
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
467-530 |
5.06e-30 |
|
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 113.39 E-value: 5.06e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 63054498 467 QVLNRYTFASTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSY 530
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
382-1170 |
1.91e-27 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 121.65 E-value: 1.91e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 382 DDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQkcVETNREFNLTLAVKSNIITNGLRyslatgnwgdqkrSMVN 461
Cdd:PRK14844 464 DDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMS--TSSLDKVSPSDFINPKVLTNVLR-------------DFFN 528
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 462 RVGVSQVLNRYTFASTLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSvgsps 537
Cdd:PRK14844 529 SSQLSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN----- 603
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 538 apiiefleewgletleDYNPSASPnATKVfvngvwlgVHRDPAHLTETLRSLRRRLDISAEVSIVRDirekELRLFTDAG 617
Cdd:PRK14844 604 ----------------KYGFIESP-YRKV--------VNRVVTDQIEYLSAIDEGLYYIADTSAKLD----ENNCFVDDM 654
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 618 RICRplfivdnnpnserrgelcirkehiqqliedkdrydidpeqRFGWTALVSSGLIEYLDAEEEETVMIAMS--P--ED 693
Cdd:PRK14844 655 LYCR----------------------------------------YAGSFVMVSSDQVSYIDVSPKQVISVAASliPflEN 694
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 694 LEASRQMQaGYEVKEELDPAqrVKPAPnPHVHAWTHCEIHP---AMILGILASIIPFPDHNQSPRNTYQSAmGKQAMGV- 769
Cdd:PRK14844 695 DDANRALM-GSNMQRQAVPL--LKPTA-PLVATGMESFVASgsgAVVLAKRDGIVDSSDSNSIVIRAFDKE-RVNYLDVd 769
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 770 --YLTNYQ-VRMDTMANilyypQKPLatTRSMEYLK------------FRELPAGQNAIVAILCYSGYNQEDSIIMNQAS 834
Cdd:PRK14844 770 iyHLRKFQrSNHNTCIN-----QKPL--VCVGDYVKegdviadgpainSGELALGQNLLVAFMSWQGYNFEDSIIISSEV 842
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 835 IDRGLFRSIFyrtytdqekkigmtvMEEFERPVRSTTL------RMKHGTYDK----LEDDGLIAPGTRVSGEDIIIGKT 904
Cdd:PRK14844 843 VKKDLFTSIH---------------IEEFECVVHDTPLgsekitRAIPGVNEEnlyhLDDSGIVKIGTRVGPGYILVGKV 907
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 905 APIP-------------------------------------LDHEELGQR----------------TQLHAKRD------ 925
Cdd:PRK14844 908 TPKPslslppetkllmtifgeksfdcadsslytspdvegtvIDVQVFTRRgveenerallikqkeiNDFEKERDyiinvt 987
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 926 ----------------------------------------VSTPLRSTESGIVDQVMVTTNQ---------EGLKF---- 952
Cdd:PRK14844 988 seyfydelkkllinsgsqdrekfdsiereqwwgiglknqsISEQVKSLKKDFDEKVSHAIAQfkrkveklhEGYDLpqgv 1067
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 953 ---VKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQL--------S 1021
Cdd:PRK14844 1068 smsVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVgwackklgE 1147
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1022 KVSAL--------SGF--------EGDATPF------------------------------------------------- 1036
Cdd:PRK14844 1148 KVGNIldeinkikSAFckgirslnDDNFTKFaaayldnkkienidddeitasvlntpnknalndelnelvenylnscksa 1227
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1037 ---------------TDVTV-----------------------------------EAVSKLLRSHGFQSRGFEVMYHGHT 1066
Cdd:PRK14844 1228 ysnlrnflievyscgSNVSIcnnirdisdnnliefarklrdgipvaapvfegpkdEQIAKLFELAGLDNSGQAVLYDGCS 1307
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 1067 GRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSDa 1146
Cdd:PRK14844 1308 GEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD- 1386
|
1050 1060
....*....|....*....|....*..
gi 63054498 1147 yrvivcDICGLIAI--ASYKKDS-YEC 1170
Cdd:PRK14844 1387 ------DINGRVKIyeSIIKGDSnFEC 1407
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
665-734 |
1.47e-22 |
|
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.
Pssm-ID: 428013 [Multi-domain] Cd Length: 53 Bit Score: 91.83 E-value: 1.47e-22
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054498 665 WTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYevkeeldpaqrvkpapnPHVHAWTHCEIHP 734
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG-----------------PYAHTYTHCEIHP 53
|
|
| |
