|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
37-1130 |
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: 1069.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 37 LVKAHIESFDQAVTDGLCRVVEAIPPMEFLYKGDRISLSFVEAIIHTPSVSKGGISRdlRVFPAECRGRRCTYRAKLVAD 116
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEGGVTR--KLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 117 VSWSVNGVPK-GIIKQSLGQMPIMVKSKLCNLHGLSPKELLEHHEEAEEMGGYFIVNGIEKVIRLLIMPRRNYPI----A 191
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 192 VSRPKFKSRGQGYTQYAISMRCVKEEH-TAINMNLHYLDNgtvmvnfiyrkelfflplgfalkalvdysdyqiyqelikg 270
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKkKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 271 REDnsfykscvsemlrivmdqgcttkikVLNYLGERFrvklnlpewftheqcahflldeclcihlktdvekfYMLCLMTR 350
Cdd:cd00653 199 QEE-------------------------ALKYIGKRF-----------------------------------EDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 351 KLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKMEGWLVSVKLALEKKPQRVGGLTPdsmtKLFNMGTDLTKAFEY 430
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTP----QLLINSKPITSGIKE 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 431 LLATGNLMSKTGlgMLQNSGLCVVADKLNFIRYLSHFRCVHRGAAFAKMRTTTVRKLLPESWGFLCPVHTPDGEPCGLMN 510
Cdd:cd00653 295 FLATGNWGSKRF--LMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVK 372
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 511 HMTAHCEIVapvyptstlpgllcslgvnaadgnpgqaysdcypvildgamigwvekevapsvieslrrfkvlgekkvppw 590
Cdd:cd00653 373 NLALMARIS----------------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 591 teivlvpqtgkaslypglylfttpcrmvrtvrnlslgkqeliGIFEQVYLNVgifekeieDGVTTHQELFPHSMLSVVAE 670
Cdd:cd00653 382 ------------------------------------------GRIERPYRIV--------EKEVTHIEISPSQILSVAAS 411
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 671 FIPFSDHNQSPRNMYQCQMSKQTMGFPLHSYQYRSDNKLYRLQTPQSPLVRPAMYDHYDVDNYPIGTNAIVAVISYTGYD 750
Cdd:cd00653 412 LIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYN 491
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 751 MEDAMIVNKSSWERGFAHGSVYKTEIIDLSEKVKGDDSIVFGVKPG-DPKVMGKLDADGLPFIGSVLKYGDPFYGYISLN 829
Cdd:cd00653 492 FEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNvSEEKLKNLDEDGIIRPGARVEPGDILVGKITPK 571
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 830 TGQSHVY--------------FYKYQESCVVDNIKVCSNETGTGRFKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWP 895
Cdd:cd00653 572 GETESTPifgekardvrdtslKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 896 AEDMPFTESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTFSEENSALEHFGEllkaAGYNYYGTER 975
Cdd:cd00653 652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEV 727
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 976 LYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRL 1055
Cdd:cd00653 728 LYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERL 807
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2055117661 1056 FNCSDRSVAQVCMDCGSLLSPLLekpppnwsatrhrktiCLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLD 1130
Cdd:cd00653 808 TIKSDDVVARVCVKCGIILSANL----------------CRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
37-1132 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 574.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 37 LVKAHIESFDQAVTDGLCRVVEAIPPMEFLYKGDRISLSFVEaiIHTPSV--SKGGisrDLRVFPAECRGRRCTYRAKLV 114
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVLGKIR--VGEPEIkeADGS---ERPITPMEARLRNLTYAAPLY 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 115 ADVSWSVNGVPKGIIKQSLGQMPIMVKSKLCNLHGLSPKELLEHHEEAEEMGGYFIVNGIEKVI---------RLLIMPR 185
Cdd:PRK08565 89 LTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIvsqedlapnRVLVDKG 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 186 RNYPIAVSRPKFKSRGQGYTQYAIsmrcvkeehtainmnLHYLDNGTVMVNF--IYRKelffLPLGFALKAL-------- 255
Cdd:PRK08565 169 EAGSSITHTAKVISSRAGYRAQVT---------------VERRKDGTIYVSFpaVPGK----IPFVILMRALgletdrdi 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 256 VD--YSDYQIYQELIKGREDNSfykscvsemlrivmdQGCTTKIKVLNYLGERFRVKLNLPEwftHEQCAHFLLDECLCI 333
Cdd:PRK08565 230 VYavSLDPEIQQELLPSLEQAS---------------SIAATVEDALDYIGKRVAIGQPREY---RIERAEQILDKYLLP 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 334 HLKTDVE----KFYMLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKMEGWLVSVKLALEKKPQRVGGL 409
Cdd:PRK08565 292 HLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKL 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 410 TPDSMTKlfnmgTD-LTKAFEYLLATGNLM-SKTGLGMLqnsglcvvADKLNFIRYLSHFRCV----HRGAA-FAkmrtt 482
Cdd:PRK08565 372 DLRAIVR-----PDiITERIRHALATGNWVgGRTGVSQL--------LDRTNYLSTLSHLRRVvsplSRGQPhFE----- 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 483 tVRKLLPESWGFLCPVHTPDGEPCGLMNHMTAHCEIVAPVyPTSTLPGLLCSLGVNAADGNPGQAYSDCYPVILDGAMIG 562
Cdd:PRK08565 434 -ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGV-DEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIG 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 563 WVE--KEVAPSVIESLRRFKVLGEKKV-----PPWTEI------------VLVPQTGKASLYP--------GLYLFTTPC 615
Cdd:PRK08565 512 YHPdgEELAEKIRELRRSGKISDEVNVayietGEINEVyvncdsgrvrrpLIVVENGKPKLTRehveklkkGELTFDDLV 591
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 616 RMvrtvrnlslGKQELIGIFEQVYLNVGIFEKEIEDGvTTHQELFPHSMLSVVAEFIPFSDHNQSPRNMYQCQMSKQTMG 695
Cdd:PRK08565 592 KM---------GVIEYLDAEEEENAYVALDPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 696 FPLHSYQYRSDNKLYRLQTPQSPLVRPAMYDHYDVDNYPIGTNAIVAVISYTGYDMEDAMIVNKSSWERGFAHGS---VY 772
Cdd:PRK08565 662 LYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTffrTY 741
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 773 KTE----IIDLSEKVKGDDSIVFGVKPgdPKVMGKLDADGLPFIGSVLKYGDPFYGYIS------LNTGQSHVYFYK--- 839
Cdd:PRK08565 742 ETEerkyPGGQEDKIEIPEPNVRGYRG--EEYYRKLDEDGIVSPEVEVKGGDVLIGKTSpprfleELEELSLGLQERrdt 819
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 840 -----YQESCVVDNIKVCSNETGTgrfKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNP 914
Cdd:PRK08565 820 svtvrHGEKGIVDTVLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINP 896
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 915 HGFPSRMTIGMLIESMAGKSASLHGLCHDATPFtfseENSALEHFGELLKAAGYNYYGTERLYSGLSGLELEADIFIGVV 994
Cdd:PRK08565 897 HAIPSRMTVGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVV 972
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 995 YYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAQVCMDCGSll 1074
Cdd:PRK08565 973 YYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH-- 1050
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*...
gi 2055117661 1075 spllekppPNWSATRHRKTICLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLDVK 1132
Cdd:PRK08565 1051 --------IAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
668-1026 |
5.58e-172 |
|
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: 510.15 E-value: 5.58e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 668 VAEFIPFSDHNQSPRNMYQCQMSKQTMGFPLHSYQYRSDNKLYRLQTPQSPLVRPAMYDHYDVDNYPIGTNAIVAVISYT 747
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 748 GYDMEDAMIVNKSSWERGFAHGSVYKTeiIDLSEKVKGDDSIVFGVKPGDP-KVMGKLDADGLPFIGSVLKYGDPFYGYI 826
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPIEEITRDIPNVSeEALKKLDEDGIVRVGAEVKPGDILVGKV 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 827 S---------------LNTGQSHVYFYKYQESCVVDNIKVCsnETGTGRFKRICVTSRVPRNPTIGDKFASRHGQKGILS 891
Cdd:pfam00562 159 GpteltkllraifgekARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVS 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 892 RLWPAEDMPFTESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTFSEENsaLEHFGELLKAAGYNYY 971
Cdd:pfam00562 237 RILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*
gi 2055117661 972 GTERLYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGR 1026
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
554-1132 |
8.31e-143 |
|
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: 442.93 E-value: 8.31e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 554 VILDGAMIGWVE--KEVAPSVIEsLRRfkvlgEKKVPPWTEIVLVPQTGKaslypgLYLFTTPCRMVRT----------- 620
Cdd:TIGR03670 1 VYLNGRLIGYHDdpEELVEEVRK-LRR-----SGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivvengkpkl 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 621 ----VRNLSLGK---QELI--GIFEqvYLN--------VGIFEKEIEDGvTTHQELFPHSMLSVVAEFIPFSDHNQSPRN 683
Cdd:TIGR03670 69 trehVEKLKEGEltwDDLVkqGVIE--YLDaeeeenayIALDPEELTPE-HTHLEIDPSAILGIIASTIPYPEHNQSPRN 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 684 MYQCQMSKQTMGFPLHSYQYRSDNKLYRLQTPQSPLVRPAMYDHYDVDNYPIGTNAIVAVISYTGYDMEDAMIVNKSSWE 763
Cdd:TIGR03670 146 TMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIE 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 764 RGFAHGSVYKT-EIID------LSEKVKGDDSIVFGVKPgdPKVMGKLDADGLPFIGSVLKYGDPFYGYIS--------L 828
Cdd:TIGR03670 226 RGLARSTFFRTyEAEErrypggQEDRFEIPEPDVRGYRG--EEAYKHLDEDGIVYPEVEVKGGDVLIGKTSpprfleelR 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 829 NTGQSHV------YFYKYQESCVVDNIKVCSNETGTgrfKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFT 902
Cdd:TIGR03670 304 EFGLVTErrrdtsVTVRHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFT 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 903 ESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTfsEENsaLEHFGELLKAAGYNYYGTERLYSGLSG 982
Cdd:TIGR03670 381 EDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFE--GEP--EEELRKELLKLGFKPDGKEVMYDGITG 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 983 LELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRS 1062
Cdd:TIGR03670 457 EKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKY 536
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 1063 VAQVCMDCGSLlspllekpppNWSATRHRKTICLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLDVK 1132
Cdd:TIGR03670 537 VVYVCENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
655-1129 |
1.25e-98 |
|
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: 335.93 E-value: 1.25e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 655 THQELFPHSMLSVVAEFIPFSDHNQSPRNMYQCQMSKQTMGFPLHSYQYrsdnKLYRLQT----------PQSPLVR--- 721
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----LHYPLQKfqrsnqgtciNQRPIVRvgd 586
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 722 -----------PAMydhyDVDNYPIGTNAIVAVISYTGYDMEDAMIVNKSSWERGFA---HGSVYKTEIIDlsekVKGDD 787
Cdd:COG0085 587 rvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLtsiHIEEYEIEARD----TKLGP 658
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 788 SIVFGVKPGD-PKVMGKLDADGLPFIGSVLKYGDPFYGYISL--NTGQS------HVYFY-KYQ------------ESCV 845
Cdd:COG0085 659 EEITRDIPNVsEEALRNLDEDGIIRIGAEVKGGDILVGKVTPkgETELTpeerllRAIFGeKARevrdtslrvphgEKGK 738
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 846 VDNIKVCSNETG----TGRFKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNPHGFPSRM 921
Cdd:COG0085 739 VIDVKVFSREEGdelpPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRM 818
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 922 TIGMLIESMAGKSASLHGLCHDATPFtFSEENSALEhfgELLKAAGYNYYGTERLYSGLSGLELEADIFIGVVYYQRLRH 1001
Cdd:COG0085 819 NVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIR---ELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHH 894
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 1002 MVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAQVCMdcgsllspllekp 1081
Cdd:COG0085 895 MVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV------------- 961
|
490 500 510 520
....*....|....*....|....*....|....*....|....*...
gi 2055117661 1082 ppnWSATRhrkticllcnKSDSIETVSVPYVFKYFVAELAAMNIKIKL 1129
Cdd:COG0085 962 ---YEAIV----------KGENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
561-619 |
1.25e-25 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
Pssm-ID: 462028 Cd Length: 58 Bit Score: 100.64 E-value: 1.25e-25
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 2055117661 561 IGWVEKEVAPSVIESLRRFKVLGEKKVPPWTEIVLVPQTgKASLYPGLYLFTTPCRMVR 619
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
37-1130 |
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: 1069.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 37 LVKAHIESFDQAVTDGLCRVVEAIPPMEFLYKGDRISLSFVEAIIHTPSVSKGGISRdlRVFPAECRGRRCTYRAKLVAD 116
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEGGVTR--KLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 117 VSWSVNGVPK-GIIKQSLGQMPIMVKSKLCNLHGLSPKELLEHHEEAEEMGGYFIVNGIEKVIRLLIMPRRNYPI----A 191
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 192 VSRPKFKSRGQGYTQYAISMRCVKEEH-TAINMNLHYLDNgtvmvnfiyrkelfflplgfalkalvdysdyqiyqelikg 270
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKkKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 271 REDnsfykscvsemlrivmdqgcttkikVLNYLGERFrvklnlpewftheqcahflldeclcihlktdvekfYMLCLMTR 350
Cdd:cd00653 199 QEE-------------------------ALKYIGKRF-----------------------------------EDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 351 KLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKMEGWLVSVKLALEKKPQRVGGLTPdsmtKLFNMGTDLTKAFEY 430
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTP----QLLINSKPITSGIKE 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 431 LLATGNLMSKTGlgMLQNSGLCVVADKLNFIRYLSHFRCVHRGAAFAKMRTTTVRKLLPESWGFLCPVHTPDGEPCGLMN 510
Cdd:cd00653 295 FLATGNWGSKRF--LMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVK 372
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 511 HMTAHCEIVapvyptstlpgllcslgvnaadgnpgqaysdcypvildgamigwvekevapsvieslrrfkvlgekkvppw 590
Cdd:cd00653 373 NLALMARIS----------------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 591 teivlvpqtgkaslypglylfttpcrmvrtvrnlslgkqeliGIFEQVYLNVgifekeieDGVTTHQELFPHSMLSVVAE 670
Cdd:cd00653 382 ------------------------------------------GRIERPYRIV--------EKEVTHIEISPSQILSVAAS 411
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 671 FIPFSDHNQSPRNMYQCQMSKQTMGFPLHSYQYRSDNKLYRLQTPQSPLVRPAMYDHYDVDNYPIGTNAIVAVISYTGYD 750
Cdd:cd00653 412 LIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYN 491
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 751 MEDAMIVNKSSWERGFAHGSVYKTEIIDLSEKVKGDDSIVFGVKPG-DPKVMGKLDADGLPFIGSVLKYGDPFYGYISLN 829
Cdd:cd00653 492 FEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNvSEEKLKNLDEDGIIRPGARVEPGDILVGKITPK 571
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 830 TGQSHVY--------------FYKYQESCVVDNIKVCSNETGTGRFKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWP 895
Cdd:cd00653 572 GETESTPifgekardvrdtslKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 896 AEDMPFTESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTFSEENSALEHFGEllkaAGYNYYGTER 975
Cdd:cd00653 652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEV 727
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 976 LYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRL 1055
Cdd:cd00653 728 LYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERL 807
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2055117661 1056 FNCSDRSVAQVCMDCGSLLSPLLekpppnwsatrhrktiCLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLD 1130
Cdd:cd00653 808 TIKSDDVVARVCVKCGIILSANL----------------CRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
37-1132 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 574.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 37 LVKAHIESFDQAVTDGLCRVVEAIPPMEFLYKGDRISLSFVEaiIHTPSV--SKGGisrDLRVFPAECRGRRCTYRAKLV 114
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVLGKIR--VGEPEIkeADGS---ERPITPMEARLRNLTYAAPLY 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 115 ADVSWSVNGVPKGIIKQSLGQMPIMVKSKLCNLHGLSPKELLEHHEEAEEMGGYFIVNGIEKVI---------RLLIMPR 185
Cdd:PRK08565 89 LTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIvsqedlapnRVLVDKG 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 186 RNYPIAVSRPKFKSRGQGYTQYAIsmrcvkeehtainmnLHYLDNGTVMVNF--IYRKelffLPLGFALKAL-------- 255
Cdd:PRK08565 169 EAGSSITHTAKVISSRAGYRAQVT---------------VERRKDGTIYVSFpaVPGK----IPFVILMRALgletdrdi 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 256 VD--YSDYQIYQELIKGREDNSfykscvsemlrivmdQGCTTKIKVLNYLGERFRVKLNLPEwftHEQCAHFLLDECLCI 333
Cdd:PRK08565 230 VYavSLDPEIQQELLPSLEQAS---------------SIAATVEDALDYIGKRVAIGQPREY---RIERAEQILDKYLLP 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 334 HLKTDVE----KFYMLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKMEGWLVSVKLALEKKPQRVGGL 409
Cdd:PRK08565 292 HLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKL 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 410 TPDSMTKlfnmgTD-LTKAFEYLLATGNLM-SKTGLGMLqnsglcvvADKLNFIRYLSHFRCV----HRGAA-FAkmrtt 482
Cdd:PRK08565 372 DLRAIVR-----PDiITERIRHALATGNWVgGRTGVSQL--------LDRTNYLSTLSHLRRVvsplSRGQPhFE----- 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 483 tVRKLLPESWGFLCPVHTPDGEPCGLMNHMTAHCEIVAPVyPTSTLPGLLCSLGVNAADGNPGQAYSDCYPVILDGAMIG 562
Cdd:PRK08565 434 -ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGV-DEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIG 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 563 WVE--KEVAPSVIESLRRFKVLGEKKV-----PPWTEI------------VLVPQTGKASLYP--------GLYLFTTPC 615
Cdd:PRK08565 512 YHPdgEELAEKIRELRRSGKISDEVNVayietGEINEVyvncdsgrvrrpLIVVENGKPKLTRehveklkkGELTFDDLV 591
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 616 RMvrtvrnlslGKQELIGIFEQVYLNVGIFEKEIEDGvTTHQELFPHSMLSVVAEFIPFSDHNQSPRNMYQCQMSKQTMG 695
Cdd:PRK08565 592 KM---------GVIEYLDAEEEENAYVALDPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 696 FPLHSYQYRSDNKLYRLQTPQSPLVRPAMYDHYDVDNYPIGTNAIVAVISYTGYDMEDAMIVNKSSWERGFAHGS---VY 772
Cdd:PRK08565 662 LYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTffrTY 741
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 773 KTE----IIDLSEKVKGDDSIVFGVKPgdPKVMGKLDADGLPFIGSVLKYGDPFYGYIS------LNTGQSHVYFYK--- 839
Cdd:PRK08565 742 ETEerkyPGGQEDKIEIPEPNVRGYRG--EEYYRKLDEDGIVSPEVEVKGGDVLIGKTSpprfleELEELSLGLQERrdt 819
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 840 -----YQESCVVDNIKVCSNETGTgrfKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNP 914
Cdd:PRK08565 820 svtvrHGEKGIVDTVLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINP 896
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 915 HGFPSRMTIGMLIESMAGKSASLHGLCHDATPFtfseENSALEHFGELLKAAGYNYYGTERLYSGLSGLELEADIFIGVV 994
Cdd:PRK08565 897 HAIPSRMTVGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVV 972
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 995 YYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAQVCMDCGSll 1074
Cdd:PRK08565 973 YYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH-- 1050
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*...
gi 2055117661 1075 spllekppPNWSATRHRKTICLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLDVK 1132
Cdd:PRK08565 1051 --------IAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
668-1026 |
5.58e-172 |
|
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: 510.15 E-value: 5.58e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 668 VAEFIPFSDHNQSPRNMYQCQMSKQTMGFPLHSYQYRSDNKLYRLQTPQSPLVRPAMYDHYDVDNYPIGTNAIVAVISYT 747
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 748 GYDMEDAMIVNKSSWERGFAHGSVYKTeiIDLSEKVKGDDSIVFGVKPGDP-KVMGKLDADGLPFIGSVLKYGDPFYGYI 826
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPIEEITRDIPNVSeEALKKLDEDGIVRVGAEVKPGDILVGKV 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 827 S---------------LNTGQSHVYFYKYQESCVVDNIKVCsnETGTGRFKRICVTSRVPRNPTIGDKFASRHGQKGILS 891
Cdd:pfam00562 159 GpteltkllraifgekARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVS 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 892 RLWPAEDMPFTESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTFSEENsaLEHFGELLKAAGYNYY 971
Cdd:pfam00562 237 RILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*
gi 2055117661 972 GTERLYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGR 1026
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
554-1132 |
8.31e-143 |
|
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: 442.93 E-value: 8.31e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 554 VILDGAMIGWVE--KEVAPSVIEsLRRfkvlgEKKVPPWTEIVLVPQTGKaslypgLYLFTTPCRMVRT----------- 620
Cdd:TIGR03670 1 VYLNGRLIGYHDdpEELVEEVRK-LRR-----SGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivvengkpkl 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 621 ----VRNLSLGK---QELI--GIFEqvYLN--------VGIFEKEIEDGvTTHQELFPHSMLSVVAEFIPFSDHNQSPRN 683
Cdd:TIGR03670 69 trehVEKLKEGEltwDDLVkqGVIE--YLDaeeeenayIALDPEELTPE-HTHLEIDPSAILGIIASTIPYPEHNQSPRN 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 684 MYQCQMSKQTMGFPLHSYQYRSDNKLYRLQTPQSPLVRPAMYDHYDVDNYPIGTNAIVAVISYTGYDMEDAMIVNKSSWE 763
Cdd:TIGR03670 146 TMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIE 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 764 RGFAHGSVYKT-EIID------LSEKVKGDDSIVFGVKPgdPKVMGKLDADGLPFIGSVLKYGDPFYGYIS--------L 828
Cdd:TIGR03670 226 RGLARSTFFRTyEAEErrypggQEDRFEIPEPDVRGYRG--EEAYKHLDEDGIVYPEVEVKGGDVLIGKTSpprfleelR 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 829 NTGQSHV------YFYKYQESCVVDNIKVCSNETGTgrfKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFT 902
Cdd:TIGR03670 304 EFGLVTErrrdtsVTVRHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFT 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 903 ESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTfsEENsaLEHFGELLKAAGYNYYGTERLYSGLSG 982
Cdd:TIGR03670 381 EDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFE--GEP--EEELRKELLKLGFKPDGKEVMYDGITG 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 983 LELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRS 1062
Cdd:TIGR03670 457 EKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKY 536
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 1063 VAQVCMDCGSLlspllekpppNWSATRHRKTICLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLDVK 1132
Cdd:TIGR03670 537 VVYVCENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
553-1132 |
5.56e-130 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 409.35 E-value: 5.56e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 553 PVILDGAMIGWVEKEVApsVIESLRRFKVLGEkkVPPWTEIVLVPQTGKaslypgLYLFTTPCRMVR---TVRN------ 623
Cdd:PRK07225 6 KVYVNGKLIGTHDDPEE--LVEEIREARRSGE--ISEEVNVSYKEETNE------VIINTDAGRARRpliVVENgepllt 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 624 -----------------LSLGKQELIGIFEQVYLNVGIFEKEIEDGvTTHQELFPHSMLSVVAEFIPFSDHNQSPRNMYQ 686
Cdd:PRK07225 76 eehieklkngeltfddlVKQGVIEYLDAEEEENAYIAVYEEDLTEE-HTHLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 687 CQMSKQTMGFPLHSYQYRSDNKLYRLQTPQSPLVRPAMYDHYDVDNYPIGTNAIVAVISYTGYDMEDAMIVNKSSWERGF 766
Cdd:PRK07225 155 AGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 767 AHGSVYKT-EIID------LSEKVKGDDSIVFGVKPGDpkVMGKLDADGLPFIGSVLKYGDPFYGYIS--------LNTG 831
Cdd:PRK07225 235 GRSHFFRTyEGEErrypggQEDRFEIPDKDVRGYRGEE--AYRHLDEDGLVNPETEVKEGDVLIGKTSpprfleepDDFG 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 832 QShvyfyKYQ-----------ESCVVDNIKVCSNETGTGRFKricVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMP 900
Cdd:PRK07225 313 IS-----PEKrretsvtmrsgEEGIVDTVILTETEEGSRLVK---VRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMP 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 901 FTESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTFSEEnsalEHFGELLKAAGYNYYGTERLYSGL 980
Cdd:PRK07225 385 FTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDE----EDLREALEKLGFEHTGKEVMYDGI 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 981 SGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1060
Cdd:PRK07225 461 TGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 540
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2055117661 1061 RSVAQVCMDCGSLlspllekpppnwsATRHRK---TICLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLDVK 1132
Cdd:PRK07225 541 KVEIYVCAKCGMI-------------AIYDKKrnrKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELE 602
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
655-1129 |
1.25e-98 |
|
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: 335.93 E-value: 1.25e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 655 THQELFPHSMLSVVAEFIPFSDHNQSPRNMYQCQMSKQTMGFPLHSYQYrsdnKLYRLQT----------PQSPLVR--- 721
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----LHYPLQKfqrsnqgtciNQRPIVRvgd 586
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 722 -----------PAMydhyDVDNYPIGTNAIVAVISYTGYDMEDAMIVNKSSWERGFA---HGSVYKTEIIDlsekVKGDD 787
Cdd:COG0085 587 rvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLtsiHIEEYEIEARD----TKLGP 658
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 788 SIVFGVKPGD-PKVMGKLDADGLPFIGSVLKYGDPFYGYISL--NTGQS------HVYFY-KYQ------------ESCV 845
Cdd:COG0085 659 EEITRDIPNVsEEALRNLDEDGIIRIGAEVKGGDILVGKVTPkgETELTpeerllRAIFGeKARevrdtslrvphgEKGK 738
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 846 VDNIKVCSNETG----TGRFKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNPHGFPSRM 921
Cdd:COG0085 739 VIDVKVFSREEGdelpPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRM 818
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 922 TIGMLIESMAGKSASLHGLCHDATPFtFSEENSALEhfgELLKAAGYNYYGTERLYSGLSGLELEADIFIGVVYYQRLRH 1001
Cdd:COG0085 819 NVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIR---ELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHH 894
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 1002 MVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAQVCMdcgsllspllekp 1081
Cdd:COG0085 895 MVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV------------- 961
|
490 500 510 520
....*....|....*....|....*....|....*....|....*...
gi 2055117661 1082 ppnWSATRhrkticllcnKSDSIETVSVPYVFKYFVAELAAMNIKIKL 1129
Cdd:COG0085 962 ---YEAIV----------KGENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
36-402 |
6.97e-64 |
|
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: 222.26 E-value: 6.97e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 36 ELVKAHIESFDQAVTDGLCRVVEA-------IPPMEFLYKGDRISLSFVEAIIHTPSVSKGGISRDLrVFPAECRGRRCT 108
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDEnalieseFEIQHPGENGDKLSLKFGQIRLGKPMFDETDGSTRE-IYPQECRLRNLT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 109 YRAKLVADVSWSVNGVPKGI-IKQSLGQMPIMVKSKLCNLHGLSPKELLEHHEEAEEMGGYFIVNGIEKVIRLLIMPRRN 187
Cdd:pfam04563 80 YSAPLYVDLELSVYNGEDIKpIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRN 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 188 YPIAVSRPKFKSRGQGYTQYAISMRCVKEEHTA-INMnLHYLDNGTVMVNFIYRKELFflPLGFALKALVDYSDYQIYqE 266
Cdd:pfam04563 160 HPIVFKKADPKKRGSVASVRSSAEISVRPDSTSwVNV-LEYLSNGTIYFKFPYIKKEI--PIVIILRALGFTSDREIF-E 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 267 LIKGREDNSFYKSCVSEMLRIVMDQGCTTKIKVLNYLGERFRVKLNL-PEWFTHEQCAHFLLDECLCIHLKTD----VEK 341
Cdd:pfam04563 236 LICYDVNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMgRPREPRIKYAEEILQKEVLPHLGTYeldeTKK 315
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2055117661 342 FYMLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKMEGWLVSVKLALEKK 402
Cdd:pfam04563 316 AYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKV 376
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
735-1060 |
7.15e-47 |
|
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: 183.33 E-value: 7.15e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 735 IGTNAIVAVISYTGYDMEDAMIVNksswERGF---AHGSVYKTE-IIDLSEKVKGDDSIVFGVKPGDPKVMGKLDADGLP 810
Cdd:TIGR02013 673 LGRNVLVAFMPWNGYNYEDAILIS----ERLVkddVFTSIHIEEyEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIV 748
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 811 FIGSVLKYGDPFYGYIS-------------LNT--GQ--SHV-----YFYKYQESCVVDnIKVCSNETG----TGRFKRI 864
Cdd:TIGR02013 749 RIGAEVKAGDILVGKVTpkgeteltpeeklLRAifGEkaRDVrdtslRVPPGVEGTVID-VKVFSREQGdelpPGVNKLV 827
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 865 CVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNPHGFPSRMTIGMLIES---MAGKSASLHGLC 941
Cdd:TIGR02013 828 KVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAGKRLGRKGVP 907
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 942 HdATPfTFseENSALEHFGELLKAAGYNYYGTERLYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQ 1021
Cdd:TIGR02013 908 I-ATP-VF--DGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQ 983
|
330 340 350
....*....|....*....|....*....|....*....
gi 2055117661 1022 PMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1060
Cdd:TIGR02013 984 PLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
456-1060 |
1.79e-43 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 172.58 E-value: 1.79e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 456 DKLNFIRYLSH-FRCVHRGAA-FAKMRTTT-VRKLLPESWGFLCPVHTPDGEPCGLMNHMTAHCEI------VAPVYPTs 526
Cdd:CHL00207 371 DQTNPLSELTHkRRISILGPGgLDKDRISFaVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARInkfgfiETPFYKV- 449
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 527 tlpgllcslgvnaadgNPGQAYSDCYPVILDGamigwVEKE---VAPSVIeSLRRFKVLGEKKVPpwteivlvpqtgkas 603
Cdd:CHL00207 450 ----------------INGKVKKFGNPIYLTA-----DSEDlyrIAPNDI-NLNKNNYFKKNIIP--------------- 492
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 604 lypglylfttpcrmvrtVRNlslgKQE--LIGIFEQVYLNVGifekeiedgvtthqelfPHSMLSVVAEFIPFSDHNQSP 681
Cdd:CHL00207 493 -----------------VRY----KQEfkTVNPSKVDFIAIS-----------------PIQVFSIAESLIPFLEHNDAN 534
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 682 RNMYQCQMSKQTM----------------------GFPLHSYQ-----YRSDNKL-----------YRLQ---------- 713
Cdd:CHL00207 535 RALMGSNMQRQAVpllypekpivgtgyekqialdsGMTIISLTegivvSVSAYKIiiqddnnryihYYLQkyqrsnqntc 614
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 714 TPQSPLVRPA--------MYDHYDVDN--YPIGTNAIVAVISYTGYDMEDAMIVNKS-SWERGFA--HGSVYKteiIDLS 780
Cdd:CHL00207 615 INYRPIVWVGekinigqiLADGSDIDNseLALGQNVLVAYMPWEGYNFEDAILINKRlVYEDLFTsiHIEKYE---IELR 691
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 781 EKVKGDDSIVFGVKPGDPKVMGKLDADGLPFIGSVLKYGDPFYGYISLNTGQSHVYFYKY-------------------- 840
Cdd:CHL00207 692 QTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLlraifgekakdvkdtslrmp 771
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 841 --QESCVVDnIKVCSNETGT----GRFKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNP 914
Cdd:CHL00207 772 ngGYGRVIK-VEIFSRSKGDelkfGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNP 850
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 915 HGFPSRMTIGMLIESMAGKSAslHGLCHDATPFTFSEENSAL-------EHFGELLKAAG----YNYY--GTERLYSGLS 981
Cdd:CHL00207 851 LGVPSRMNVGQLFECLLGLAG--DNLNKRFKILPFDEMYGSEysrilinNKLNQASIKNNeywlFNSYhpGKMVLRDGRT 928
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2055117661 982 GLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1060
Cdd:CHL00207 929 GYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD 1007
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
875-1051 |
1.59e-36 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 150.25 E-value: 1.59e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 875 TIGDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNPHGFPSRMTIGMLIES---MAGKsaslhGL-CHDATP-Ftf 949
Cdd:PRK00405 881 QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAAK-----GLgIKFATPvF-- 953
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 950 seENSALEHFGELLKAAGYNYYGTERLYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQ 1029
Cdd:PRK00405 954 --DGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQF 1031
|
170 180
....*....|....*....|..
gi 2055117661 1030 GGIRFGEMERDALLAHGTSFLL 1051
Cdd:PRK00405 1032 GGQRFGEMEVWALEAYGAAYTL 1053
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
453-517 |
5.68e-33 |
|
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: 121.86 E-value: 5.68e-33
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2055117661 453 VVADKLNFIRYLSHFRCVH--RGAAFAKMRTTTVRKLLPESWGFLCPVHTPDGEPCGLMNHMTAHCE 517
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNspRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
736-1060 |
2.38e-30 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 130.02 E-value: 2.38e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 736 GTNAIVAVISYTGYDMEDAMIVNksswERgfahgSVYK---TEI------IDLSEKVKGDDSIVFGVKPGDPKVMGKLDA 806
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLIS----ER-----LVYEdiyTSFhirkyeIQTHVTSQGPERITKEIPHLEAHLLRNLDK 722
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 807 DGLPFIGSVLKYGDPFYGYISLNTGQSHVYF--------------YKYQESC----------VVDNIKVCSNETGTGRFK 862
Cdd:CHL00001 723 NGIVMLGSWVETGDILVGKLTPQEAEESSYApegrllraifgiqvSTSKETClklpiggrgrVIDVRWIQKKGGSSYNPE 802
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 863 RICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCH 942
Cdd:CHL00001 803 TIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHY 882
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 943 DATPF--TFSEENSALEHFGELLKA---AGY------NYYGTERLYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRT 1011
Cdd:CHL00001 883 RIAPFdeRYEQEASRKLVFSELYEAskqTANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARS 962
|
330 340 350 360
....*....|....*....|....*....|....*....|....*....
gi 2055117661 1012 TGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1060
Cdd:CHL00001 963 SGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
37-519 |
4.93e-29 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 122.75 E-value: 4.93e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 37 LVKAHIESFDQAVTDGLCRVVEAIPPMEFLYkGDRISLSFVEAIIHTPSV--SKGGISRdlrVFPAECRGRRCTYRAKLV 114
Cdd:PRK09606 18 LVRHHIDSYNDFVDNGLQKIIDEQGPIETEI-EDGVYVELGKIRVGKPVVkeADGSERE---IYPMEARLRNLTYSAPLY 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 115 ADVSWSVNGVPKGIIKQSLGQMPIMVKSKLCNLHGLSPKELLEHHEEAEEMGGYFIVNGIEKVIRLL--IMPRR------ 186
Cdd:PRK09606 94 LEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLedLAPNKilvekd 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 187 ---NYPIAVSrpKFKSRGQGYtqyaiSMRCVKEEHTainmnlhyldNGTVMVNFIY-RKELFFLPLgfaLKALVDYSDyq 262
Cdd:PRK09606 174 eryGDRIEVA--KVFSQRRGY-----RALVTVERNR----------DGLLEVSFPSvPGSIPFVIL---MRALGLETD-- 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 263 iyQELIKGREDNSFYkscVSEMLRIVMDQGCTTKIKVLNYLGErfRVKLNLPEWFTHEQcAHFLLDECLCIHLKTDVEKF 342
Cdd:PRK09606 232 --EEIVEAVSDDPEI---VKFMLENLEEAEVDTQEEALEYIGK--RVAPGQTKEYRIKR-AEYVIDRYLLPHLGVEPEVR 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 343 ----YMLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQL--------YLMFLKEkmegwlvsVKLALEKKPQRvgglt 410
Cdd:PRK09606 304 rakaHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLmedlfrvaFNRLARD--------VKYQLERANMR----- 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 411 pdsmTKLFNMGT----D-LTKAFEYLLATGNLMS-KTGLGMLqnsglcvvADKLNFIRYLSHFRCV---------HRGAa 475
Cdd:PRK09606 371 ----NRELSIKTavrsDvLTERLEHAMATGNWVGgRTGVSQL--------LDRTDYMATLSHLRRVvsplsrsqpHFEA- 437
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 2055117661 476 fakmrtttvRKLLPESWGFLCPVHTPDGEPCGLMNHMTAHCEIV 519
Cdd:PRK09606 438 ---------RDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEIS 472
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
858-1060 |
2.41e-27 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 121.18 E-value: 2.41e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 858 TGRFKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNPHGFPSRMTIGMLIE---SMAGK- 933
Cdd:PRK09603 1072 NGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEmhlGLVGKe 1151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 934 -----------------------------------SASLHGL--CHDATPFTFSE-------------ENSALEHFGELL 963
Cdd:PRK09603 1152 fgkqiasmledktkdfakelrakmleianainekdPLTIHALenCSDEELLEYAKdwskgvkmaipvfEGISQEKFYKLF 1231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 964 KAAGYNYYGTERLYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALL 1043
Cdd:PRK09603 1232 ELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALE 1311
|
250
....*....|....*..
gi 2055117661 1044 AHGTSFLLHDRLFNCSD 1060
Cdd:PRK09603 1312 AYGAAHTLKEMLTIKSD 1328
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
561-619 |
1.25e-25 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
Pssm-ID: 462028 Cd Length: 58 Bit Score: 100.64 E-value: 1.25e-25
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 2055117661 561 IGWVEKEVAPSVIESLRRFKVLGEKKVPPWTEIVLVPQTgKASLYPGLYLFTTPCRMVR 619
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1030-1132 |
3.49e-22 |
|
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: 91.88 E-value: 3.49e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 1030 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAQVCMDCGSLLSpllekpppnwsatrhrKTICLLCNKSDSIETVSV 1109
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAA----------------YNKCPICKGETDISPGYI 64
|
90 100
....*....|....*....|...
gi 2055117661 1110 PYVFKYFVAELAAMNIKIKLDVK 1132
Cdd:pfam04560 65 PESFKLLFQELQSLGIDPRLLLE 87
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
877-1060 |
8.35e-21 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 99.70 E-value: 8.35e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 877 GDKFASRHGQKGILSRLWPAEDMPFTESGMSPDILFNPHGFPSRMTIGMLIESMAG------------------------ 932
Cdd:PRK14844 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgekvgnildeinkiksaf 1163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 933 -------------KSASLH------------------------------------------------------------- 938
Cdd:PRK14844 1164 ckgirslnddnftKFAAAYldnkkienidddeitasvlntpnknalndelnelvenylnscksaysnlrnflievyscgs 1243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 939 --GLCHDATPFTFSE-------------------ENSALEHFGELLKAAGYNYYGTERLYSGLSGLELEADIFIGVVYYQ 997
Cdd:PRK14844 1244 nvSICNNIRDISDNNliefarklrdgipvaapvfEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYML 1323
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2055117661 998 RLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1060
Cdd:PRK14844 1324 KLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
185-367 |
7.51e-07 |
|
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: 50.81 E-value: 7.51e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 185 RRNYPIAVSRPKFKSRGQGYTQYAISMRCVkeehtainmnLHYLDN--GTVMVNFIYRKELffLPLGFALKALVDYSDYQ 262
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGS----------WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055117661 263 IYQELIkgrEDNSFYKSCVSEMLRIVMDQGCTTKIKVLNYLGERFRVKLNLPEWFTHEQ------------CAHFLLDEc 330
Cdd:pfam04561 69 ILDRLC---YDFNDPQMLELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAReilysrdpkynlNKHLGLNE- 144
|
170 180 190
....*....|....*....|....*....|....*..
gi 2055117661 331 lciHLKTDVEKFYMLCLMTRKLFSFAKQECMEENPDS 367
Cdd:pfam04561 145 ---PFENERLKAQDILYMIDRLLNLKLGRRKPDDIDH 178
|
|
| |
