|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-1069 |
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: 1190.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 1 MKANEKVTSDA-DPMWYLKYLNIYVGLPDVEESfNVTRPVSPHECRLRDMTYSAPITVDIEYTRGSQRIIR-NALPIGRM 78
Cdd:cd00653 21 VKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDIRLTVNDKGKIKeQEVFIGEI 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 79 PIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEaDRKGAVGASVTSSTHEKKSRTNM 158
Cdd:cd00653 100 PIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSKGKRIYTKTSIPSYSPYRGSW 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 159 AVKQGRFYLRHNTLSEDIPIviifkamgvesdqeivqmigteehvmaafgpsleecqkaqiftQMQALKYIGNKVrrqrm 238
Cdd:cd00653 179 LEVKSDKKKDRIYVRIDLKR-------------------------------------------QEEALKYIGKRF----- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 239 wgggpkktkieearellastilthvpvkefnfrakcIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFED 317
Cdd:cd00653 211 ------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 318 LFKKFNSEMKKIADQVIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRI 397
Cdd:cd00653 255 GLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRRI 332
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 398 SS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpivklasnlgvedvnllcgeelsyp 476
Cdd:cd00653 333 SSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------------------------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 477 nvflvflngnilgvirdhkklvntfrlmrragyinefvsistnltdrcvyissdgGRLCRPYIIVKKQkpavtnkhmeel 556
Cdd:cd00653 382 -------------------------------------------------------GRIERPYRIVEKE------------ 394
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 557 aqgyrnfedflheslveyldvneendcnialyehtinkdTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM 636
Cdd:cd00653 395 ---------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAV 435
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 637 GTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKN 716
Cdd:cd00653 436 GTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKK 515
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 717 AKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQpQYKDV 796
Cdd:cd00653 516 YEIELRKTKNGPEEITRGDI----PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKAR-DVRDT 590
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 797 PITYKGATDSYIEKVMISS---NAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNP 873
Cdd:cd00653 591 SLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNP 670
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 874 HGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQK 953
Cdd:cd00653 671 HGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQR 750
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 954 LKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGW 1033
Cdd:cd00653 751 LKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANL 830
|
1050 1060 1070
....*....|....*....|....*....|....*.
gi 238908505 1034 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLK 1069
Cdd:cd00653 831 CRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
17-1071 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1041.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 17 LKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAE 96
Cdd:PRK08565 49 IVLGKIRVGEPEIKEADGSERPITPMEARLRNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDE 128
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 97 FAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEADRKGA---VGASVTSSTHEKKSRTNMA-VKQGRFYLRHNTL 172
Cdd:PRK08565 129 LIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSsitHTAKVISSRAGYRAQVTVErRKDGTIYVSFPAV 208
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 173 SEDIPIVIIFKAMGVESDQEIVQMIGTEEHVMAAFGPSLEECQKAQIfTQMQALKYIGNKVRRqrmwgGGPKKTKIEEAR 252
Cdd:PRK08565 209 PGKIPFVILMRALGLETDRDIVYAVSLDPEIQQELLPSLEQASSIAA-TVEDALDYIGKRVAI-----GQPREYRIERAE 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 253 ELLASTILTHVPVKEFNFRAKCIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIAD 331
Cdd:PRK08565 283 QILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLE 362
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 332 QVIPKQRAAQFDVVkhMRQDQITNGMVNAISTGNWSlkrfkMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPR 411
Cdd:PRK08565 363 KSYARGRKLDLRAI--VRPDIITERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEAR 435
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 412 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEElsYPNVFLVFLNGNILGVI 491
Cdd:PRK08565 436 DLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYH 513
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 492 RDHKKLVNTFRLMRRAGYINEFVSISTNLTD--RCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHE 569
Cdd:PRK08565 514 PDGEELAEKIRELRRSGKISDEVNVAYIETGeiNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKM 593
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 570 SLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDT 649
Cdd:PRK08565 594 GVIEYLDAEEEENAYVALDPEDLTPEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDT 673
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 650 LMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTF 729
Cdd:PRK08565 674 RGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQE 753
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 730 DKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPITYKGATDSYI 808
Cdd:PRK08565 754 DKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKtSPPRFLEELEELSLGLQE--RRDTSVTVRHGEKGIV 831
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 809 EKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIEL 888
Cdd:PRK08565 832 DTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLES 911
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 889 LAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARG 968
Cdd:PRK08565 912 IAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARG 991
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 969 PRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCH 1042
Cdd:PRK08565 992 PVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGN 1071
|
1050 1060
....*....|....*....|....*....
gi 238908505 1043 VSSLRIPYACKLLFQELQSMNIIPRLKLS 1071
Cdd:PRK08565 1072 ISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
481-1071 |
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: 699.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 481 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 560
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 561 RNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 640
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 641 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 720
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 721 LKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPIT 799
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVTER--RRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 800 YKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSR 879
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 880 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 959
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 960 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1033
Cdd:TIGR03670 479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
|
570 580 590
....*....|....*....|....*....|....*...
gi 238908505 1034 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1071
Cdd:TIGR03670 559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
610-983 |
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: 569.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 610 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYS 689
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 690 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVL 769
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 770 VNKSMPTVTQIPLEGSNVPQQPQYKDVPITYKGATDSYIEKVMI-SSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 848
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 849 CGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLVRHGYNYL 926
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 238908505 927 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 983
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
10-1071 |
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: 567.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 10 DADPMWYLKYLNIYVGLPdveesfnvtrPVSPHECRLRDMTYSAPITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncv 88
Cdd:COG0085 44 DFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYAAPLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS---- 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 89 ltgktpaefaklnecpldpgGYFIVKGVEKVILIQEQLSKNRIIVEADRKGA---VGASVTSSTH-----EKKSRTNMAV 160
Cdd:COG0085 110 --------------------GTFIINGTERVIVSQLVRSPGVYFVEEEDKSGkdlYSAKVIPSRGawlefETDKDGTIYV 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 161 KQGRfylrhntlSEDIPIVIIFKAMGVESDQEIVQMIG---TEEHVMaafgPSLEecqKAQIFTQMQALKYIGNKVRRqr 237
Cdd:COG0085 170 RIDR--------KRKIPVTVLLRALGLETDEEILEAFGddpIQEYIL----ATLE---KDNTKTQEEALLEIYRKLRP-- 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 238 mwgGGPKKtkIEEARELLASTI-------LTHV-----------PVKEFNFRAKCIYTAVMVRRVI-LAQGDNKVDDRDY 298
Cdd:COG0085 233 ---GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLeLHLGEREPDDIDH 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 299 YGNKRLELAGQLLSLLFEDLFKKFnseMKKIADQvIPKQRAAQFDVVKHMRQDQITNGMVNAISTGNwsLKRFkMDRqgv 378
Cdd:COG0085 308 LGNRRVRLVGELLQNQFRVGLSRM---ERVVRER-MTTQDVEAITPQSLINIRPVVAAIKEFFGSSQ--LSQF-MDQ--- 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 379 TQVLSRLSY---ISALGM--MTRISSQFEktrkVsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLALMthittdmedgpi 453
Cdd:COG0085 378 TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHPSHYGRMCPIETPEGPNIGLIGSLALY------------ 438
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 454 vklasnlgvedvnllcgeelsypnvflvflngnilgvirdhkklvntfrlmrraGYINEFvsistnltdrcvyissdgGR 533
Cdd:COG0085 439 ------------------------------------------------------ARVNEY------------------GF 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 534 LCRPYIIVKKQKpaVTNKhmeelaqgyrnfedflheslVEYLDVNEENDCNIALYEHTINKDT----------------- 596
Cdd:COG0085 447 IETPYRKVENGK--VTDE--------------------IEYLTADEEENYYIAQANAPLDEDGnfleervlvryrgeevl 504
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 597 ------THLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMG-----------TIGYNQRNRIDTlmyllAYPQK 659
Cdd:COG0085 505 vppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeapllhyPLQKFQRSNQGT-----CINQR 579
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 660 PMVKT----KTIELI------EFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRY----T 725
Cdd:COG0085 580 PIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTklgpE 659
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 726 NQTFDKvmgPML-DAATRKpiwrheiLDADGICSPGEKVENKQVLVNK-SMPTVTQIPLE-----------GSNVpqqpq 792
Cdd:COG0085 660 EITRDI---PNVsEEALRN-------LDEDGIIRIGAEVKGGDILVGKvTPKGETELTPEerllraifgekAREV----- 724
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 793 yKD----VPITYKGatdsYIEKVMISSNAEDAFL-------IKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFC 861
Cdd:COG0085 725 -RDtslrVPHGEKG----KVIDVKVFSREEGDELppgvnklVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFL 799
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 862 DSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLE 941
Cdd:COG0085 800 EDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFD 879
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 942 AYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDV 1021
Cdd:COG0085 880 NPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DV 955
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|
gi 238908505 1022 CgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1071
Cdd:COG0085 956 C------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
481-542 |
2.74e-31 |
|
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: 116.70 E-value: 2.74e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 238908505 481 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 542
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
563-603 |
5.07e-10 |
|
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: 56.01 E-value: 5.07e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 238908505 563 FEDFLHESLVEYLDVNEENDCNIALYE-----------HTINKDT-THLEIEP 603
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPedleessreerEGPYAHTyTHCEIHP 53
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-1069 |
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: 1190.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 1 MKANEKVTSDA-DPMWYLKYLNIYVGLPDVEESfNVTRPVSPHECRLRDMTYSAPITVDIEYTRGSQRIIR-NALPIGRM 78
Cdd:cd00653 21 VKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDIRLTVNDKGKIKeQEVFIGEI 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 79 PIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEaDRKGAVGASVTSSTHEKKSRTNM 158
Cdd:cd00653 100 PIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSKGKRIYTKTSIPSYSPYRGSW 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 159 AVKQGRFYLRHNTLSEDIPIviifkamgvesdqeivqmigteehvmaafgpsleecqkaqiftQMQALKYIGNKVrrqrm 238
Cdd:cd00653 179 LEVKSDKKKDRIYVRIDLKR-------------------------------------------QEEALKYIGKRF----- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 239 wgggpkktkieearellastilthvpvkefnfrakcIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFED 317
Cdd:cd00653 211 ------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 318 LFKKFNSEMKKIADQVIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRI 397
Cdd:cd00653 255 GLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRRI 332
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 398 SS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpivklasnlgvedvnllcgeelsyp 476
Cdd:cd00653 333 SSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------------------------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 477 nvflvflngnilgvirdhkklvntfrlmrragyinefvsistnltdrcvyissdgGRLCRPYIIVKKQkpavtnkhmeel 556
Cdd:cd00653 382 -------------------------------------------------------GRIERPYRIVEKE------------ 394
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 557 aqgyrnfedflheslveyldvneendcnialyehtinkdTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM 636
Cdd:cd00653 395 ---------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAV 435
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 637 GTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKN 716
Cdd:cd00653 436 GTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKK 515
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 717 AKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQpQYKDV 796
Cdd:cd00653 516 YEIELRKTKNGPEEITRGDI----PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKAR-DVRDT 590
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 797 PITYKGATDSYIEKVMISS---NAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNP 873
Cdd:cd00653 591 SLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNP 670
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 874 HGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQK 953
Cdd:cd00653 671 HGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQR 750
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 954 LKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGW 1033
Cdd:cd00653 751 LKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANL 830
|
1050 1060 1070
....*....|....*....|....*....|....*.
gi 238908505 1034 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLK 1069
Cdd:cd00653 831 CRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
17-1071 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1041.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 17 LKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAE 96
Cdd:PRK08565 49 IVLGKIRVGEPEIKEADGSERPITPMEARLRNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDE 128
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 97 FAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEADRKGA---VGASVTSSTHEKKSRTNMA-VKQGRFYLRHNTL 172
Cdd:PRK08565 129 LIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSsitHTAKVISSRAGYRAQVTVErRKDGTIYVSFPAV 208
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 173 SEDIPIVIIFKAMGVESDQEIVQMIGTEEHVMAAFGPSLEECQKAQIfTQMQALKYIGNKVRRqrmwgGGPKKTKIEEAR 252
Cdd:PRK08565 209 PGKIPFVILMRALGLETDRDIVYAVSLDPEIQQELLPSLEQASSIAA-TVEDALDYIGKRVAI-----GQPREYRIERAE 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 253 ELLASTILTHVPVKEFNFRAKCIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIAD 331
Cdd:PRK08565 283 QILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLE 362
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 332 QVIPKQRAAQFDVVkhMRQDQITNGMVNAISTGNWSlkrfkMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPR 411
Cdd:PRK08565 363 KSYARGRKLDLRAI--VRPDIITERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEAR 435
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 412 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEElsYPNVFLVFLNGNILGVI 491
Cdd:PRK08565 436 DLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYH 513
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 492 RDHKKLVNTFRLMRRAGYINEFVSISTNLTD--RCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHE 569
Cdd:PRK08565 514 PDGEELAEKIRELRRSGKISDEVNVAYIETGeiNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKM 593
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 570 SLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDT 649
Cdd:PRK08565 594 GVIEYLDAEEEENAYVALDPEDLTPEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDT 673
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 650 LMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTF 729
Cdd:PRK08565 674 RGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQE 753
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 730 DKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPITYKGATDSYI 808
Cdd:PRK08565 754 DKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKtSPPRFLEELEELSLGLQE--RRDTSVTVRHGEKGIV 831
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 809 EKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIEL 888
Cdd:PRK08565 832 DTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLES 911
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 889 LAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARG 968
Cdd:PRK08565 912 IAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARG 991
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 969 PRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCH 1042
Cdd:PRK08565 992 PVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGN 1071
|
1050 1060
....*....|....*....|....*....
gi 238908505 1043 VSSLRIPYACKLLFQELQSMNIIPRLKLS 1071
Cdd:PRK08565 1072 ISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
481-1071 |
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: 699.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 481 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 560
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 561 RNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 640
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 641 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 720
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 721 LKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPIT 799
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVTER--RRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 800 YKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSR 879
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 880 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 959
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 960 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1033
Cdd:TIGR03670 479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
|
570 580 590
....*....|....*....|....*....|....*...
gi 238908505 1034 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1071
Cdd:TIGR03670 559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
481-1070 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 692.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 481 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 560
Cdd:PRK07225 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 561 RNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 640
Cdd:PRK07225 87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 641 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 720
Cdd:PRK07225 167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 721 LKRYTNQTFDKVMGPMLD--AATRKPIWRHeiLDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVP 797
Cdd:PRK07225 247 ERRYPGGQEDRFEIPDKDvrGYRGEEAYRH--LDEDGLVNPETEVKEGDVLIGKtSPPRFLEEPDDFGISPEK--RRETS 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 798 ITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFP 877
Cdd:PRK07225 323 VTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIP 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 878 SRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHM 957
Cdd:PRK07225 403 SRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHM 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 958 VLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------S 1031
Cdd:PRK07225 483 VANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIydkkrnR 562
|
570 580 590
....*....|....*....|....*....|....*....
gi 238908505 1032 GWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKL 1070
Cdd:PRK07225 563 KYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
610-983 |
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: 569.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 610 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYS 689
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 690 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVL 769
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 770 VNKSMPTVTQIPLEGSNVPQQPQYKDVPITYKGATDSYIEKVMI-SSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 848
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 849 CGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLVRHGYNYL 926
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 238908505 927 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 983
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
10-1071 |
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: 567.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 10 DADPMWYLKYLNIYVGLPdveesfnvtrPVSPHECRLRDMTYSAPITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncv 88
Cdd:COG0085 44 DFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYAAPLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS---- 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 89 ltgktpaefaklnecpldpgGYFIVKGVEKVILIQEQLSKNRIIVEADRKGA---VGASVTSSTH-----EKKSRTNMAV 160
Cdd:COG0085 110 --------------------GTFIINGTERVIVSQLVRSPGVYFVEEEDKSGkdlYSAKVIPSRGawlefETDKDGTIYV 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 161 KQGRfylrhntlSEDIPIVIIFKAMGVESDQEIVQMIG---TEEHVMaafgPSLEecqKAQIFTQMQALKYIGNKVRRqr 237
Cdd:COG0085 170 RIDR--------KRKIPVTVLLRALGLETDEEILEAFGddpIQEYIL----ATLE---KDNTKTQEEALLEIYRKLRP-- 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 238 mwgGGPKKtkIEEARELLASTI-------LTHV-----------PVKEFNFRAKCIYTAVMVRRVI-LAQGDNKVDDRDY 298
Cdd:COG0085 233 ---GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLeLHLGEREPDDIDH 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 299 YGNKRLELAGQLLSLLFEDLFKKFnseMKKIADQvIPKQRAAQFDVVKHMRQDQITNGMVNAISTGNwsLKRFkMDRqgv 378
Cdd:COG0085 308 LGNRRVRLVGELLQNQFRVGLSRM---ERVVRER-MTTQDVEAITPQSLINIRPVVAAIKEFFGSSQ--LSQF-MDQ--- 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 379 TQVLSRLSY---ISALGM--MTRISSQFEktrkVsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLALMthittdmedgpi 453
Cdd:COG0085 378 TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHPSHYGRMCPIETPEGPNIGLIGSLALY------------ 438
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 454 vklasnlgvedvnllcgeelsypnvflvflngnilgvirdhkklvntfrlmrraGYINEFvsistnltdrcvyissdgGR 533
Cdd:COG0085 439 ------------------------------------------------------ARVNEY------------------GF 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 534 LCRPYIIVKKQKpaVTNKhmeelaqgyrnfedflheslVEYLDVNEENDCNIALYEHTINKDT----------------- 596
Cdd:COG0085 447 IETPYRKVENGK--VTDE--------------------IEYLTADEEENYYIAQANAPLDEDGnfleervlvryrgeevl 504
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 597 ------THLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMG-----------TIGYNQRNRIDTlmyllAYPQK 659
Cdd:COG0085 505 vppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeapllhyPLQKFQRSNQGT-----CINQR 579
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 660 PMVKT----KTIELI------EFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRY----T 725
Cdd:COG0085 580 PIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTklgpE 659
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 726 NQTFDKvmgPML-DAATRKpiwrheiLDADGICSPGEKVENKQVLVNK-SMPTVTQIPLE-----------GSNVpqqpq 792
Cdd:COG0085 660 EITRDI---PNVsEEALRN-------LDEDGIIRIGAEVKGGDILVGKvTPKGETELTPEerllraifgekAREV----- 724
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 793 yKD----VPITYKGatdsYIEKVMISSNAEDAFL-------IKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFC 861
Cdd:COG0085 725 -RDtslrVPHGEKG----KVIDVKVFSREEGDELppgvnklVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFL 799
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 862 DSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLE 941
Cdd:COG0085 800 EDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFD 879
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 942 AYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDV 1021
Cdd:COG0085 880 NPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DV 955
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|
gi 238908505 1022 CgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1071
Cdd:COG0085 956 C------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
5-465 |
1.13e-101 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 329.22 E-value: 1.13e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 5 EKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRS 84
Cdd:PRK09606 42 GPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEARLRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGS 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 85 SNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEADRKGA---VGASVTSSTH--------EKK 153
Cdd:PRK09606 122 KICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKILVEKDERYGdriEVAKVFSQRRgyralvtvERN 201
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 154 srtnmavKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMIGTEEHVMAAFGPSLEEcqkAQIFTQMQALKYIGNKV 233
Cdd:PRK09606 202 -------RDGLLEVSFPSVPGSIPFVILMRALGLETDEEIVEAVSDDPEIVKFMLENLEE---AEVDTQEEALEYIGKRV 271
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 234 RrqrmwGGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLS 312
Cdd:PRK09606 272 A-----PGQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFeLALGRREEDDKDHYANKRLKLAGDLME 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 313 LLFEDLFKKFNSEMKKIADQVipKQRAAQFDVVKHMRQDQITNGMVNAISTGNWslkrfKMDRQGVTQVLSRLSYISALG 392
Cdd:PRK09606 347 DLFRVAFNRLARDVKYQLERA--NMRNRELSIKTAVRSDVLTERLEHAMATGNW-----VGGRTGVSQLLDRTDYMATLS 419
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 238908505 393 MMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDV 465
Cdd:PRK09606 420 HLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
8-355 |
3.03e-100 |
|
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: 322.02 E-value: 3.03e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 8 TSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTYSAPITVDIEYTR-GSQRIIRNALPIGRMPIMLRSSN 86
Cdd:pfam04563 37 PGENGDKLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNLTYSAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNA 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 87 CVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEADR---KGAVGASVTSSTHE-----KKSRTNM 158
Cdd:pfam04563 117 CILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNHPIVFKKAdpkKRGSVASVRSSAEIsvrpdSTSWVNV 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 159 A--VKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMIGTEEH---VMAAFGPSLEECQKAQIFTQMQALKYIGNKV 233
Cdd:pfam04563 197 LeyLSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELICYDVNdqqLQEELLPSLEEGFKIRIQTQEQALDYIGGRG 276
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 234 R-RQRMwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRRVIL-AQGDNKVDDRDYYGNKRLELAGQLL 311
Cdd:pfam04563 277 RaIFRM--GRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYFIGYMIRRLLLlALGRREVDDRDHLGNKRLRLAGPLL 354
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 238908505 312 SLLFEDLFKKFNSEMKKIADQVIPKQRAaqFDVVKHMRQDQITN 355
Cdd:pfam04563 355 ASLFRVLFKKLVRDVRERLQKVLGSPDD--LMLQLLVNAKPITS 396
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
40-1062 |
4.54e-66 |
|
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: 242.65 E-value: 4.54e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 40 SPHECRLRDMTYSAPITVDIEYT----RGSQRIIRNALPIGRMPIMlrssncvlTGKtpaefaklnecpldpgGYFIVKG 115
Cdd:TIGR02013 78 SVEECKERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLM--------TDR----------------GTFIING 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 116 VEKVILIQEQLSKNRIIVEADRKGAVGASVTSST----------HEKKSRTNMAVKQGRfylrhntlSEDIPIVIIFKAM 185
Cdd:TIGR02013 134 AERVVVSQLHRSPGVFFSSEKDTTKSGKVLFSARiipyrgswleFETDKKDVLYVRIDR--------KRKLPATVLLRAL 205
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 186 GVESDQEIVQMIGTEEHVMAAFgpsleecQKAQIFTQMQALKYIGNKVRrqrmwGGGPkkTKIEEARELLASTI------ 259
Cdd:TIGR02013 206 GYTIDTLILNRLGSGEYIRNTL-------RKDPTNSEEEALVEIYRKLR-----PGEP--PTVEAARSLLENLFfdpkry 271
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 260 -LTHVPVKEFNFRAK-------CIYT-----AVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLsllfEDLFKKFNSEM 326
Cdd:TIGR02013 272 dLGRVGRYKLNKKLGldvpesiGVLTkediiATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELL----QNQFRVGLARM 347
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 327 KKIAdqvipKQRAAQFDVVKHMRQDQITNGMVNAIST---GNWSLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRIS 398
Cdd:TIGR02013 348 ERIV-----RERMSTQDTDTLTPQDLINAKPISAAIKeffGSSQLSQF-MDQ---TNPLAELTHkrrLSALGPggLTRER 418
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 399 SQFEKtrkvsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmEDGPIvklasnlgvedvnllcgeELSYPNV 478
Cdd:TIGR02013 419 AGFEV-------RDVHPTHYGRICPIETPEGPNIGLINSLSTYARVN---EYGFI------------------ETPYRKV 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 479 flvflngnilgviRDHKKLVntfrlmrragyinefvsistnlTDRCVYISSDGGRlcrPYIIVKKQKPAVTNKHM-EELA 557
Cdd:TIGR02013 471 -------------KDGKVVV----------------------TDEIDYLTADEED---NYVIAQANAPLDENGRFvEDLV 512
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 558 QG-YRNFEDFLHESLVEYLDVNeendcnialyehtinkdtthleiePFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM 636
Cdd:TIGR02013 513 VArYRGEITLVSPDQVDYMDVS------------------------PKQVVSVAASLIPFLEHDDANRALMGSNMQRQAV 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 637 -------------------------------GTIGYNQRNRI---------DTLMYLLAYP--------------QKPMV 662
Cdd:TIGR02013 569 pllrseaplvgtgmeakvardsgavivakrgGVVEYVDAKRIvirydedeeEPDGGIDIYRllkyqrsnqdtcinQRPIV 648
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 663 ----KTKTIELI------EFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCT--LKRYTNQTFD 730
Cdd:TIGR02013 649 svgdRVEAGDVLadgpstDLGELALGRNVLVAFMPWNGYNYEDAILISE---------RLVKDDVFTSihIEEYEVEARD 719
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 731 KVMGP---------MLDAATRKpiwrheiLDADGICSPGEKVENKQVLVNKSMPT-VTQIPLE-----------GSNVpq 789
Cdd:TIGR02013 720 TKLGPeeitrdipnVSEEALRN-------LDENGIVRIGAEVKAGDILVGKVTPKgETELTPEekllraifgekARDV-- 790
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 790 qpqyKDVPITYKGATDSYIEKVMISSNAEDAFL-------IKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCD 862
Cdd:TIGR02013 791 ----RDTSLRVPPGVEGTVIDVKVFSREQGDELppgvnklVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLE 866
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 863 SGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRF--HYGTA-FGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEP 939
Cdd:TIGR02013 867 DGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKgvPIATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQ 946
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 940 LEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSD---- 1015
Cdd:TIGR02013 947 FDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvvg 1026
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|
gi 238908505 1016 ---AFEVDVCGQcgllgysgwchycksscHVSSLRIPYACKLLFQELQSM 1062
Cdd:TIGR02013 1027 rtkAYEAIVKGE-----------------NVPEPGIPESFNVLIKELQSL 1059
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
38-1075 |
1.62e-54 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 207.25 E-value: 1.62e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 38 PVSPHECRLRDMTYSAPITVDIEYTRGSQRIIRNA-LPIGRMPIMLRSSNCVLTGktpAEFAKLNECPLDPGGYFivkgv 116
Cdd:CHL00207 58 KYNLLSAKSYDSNYSIQIYLPLKFINLKTNKIKFInYLIGNLPKMTQRGTFIING---LERVIVSQIIRSPGIYF----- 129
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 117 EKVILiqeqlSKNRIIVEADRKGAVGASVTSSTHEKKsrtnmavkqgRFYLRHNTLSEdIPIVIIFKAMGVeSDQEIVQm 196
Cdd:CHL00207 130 KKEIK-----KNSNKIYSATLIPNRGSWIKFELDKNK----------EIWIRIDKNRK-KPLIIFLKALGL-TDQDIYS- 191
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 197 igteeHVMAAFGPSLEECQKAQI--FTQMQALKYIGNKVRRqrmwggGPKKTkIEEARELLASTILT------------- 261
Cdd:CHL00207 192 -----RLTKSEFLKKLKPILLNSnsYTNEEILLEIYKNLSP------IEPAT-VNDANQNLFSRFFDpknydlgkvgryk 259
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 262 ---HVPVKEFNFRAKCIYT---AVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSemkkiadqVIP 335
Cdd:CHL00207 260 innKLNLNIPERVRNLTYEdilSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLER--------ILR 331
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 336 KQraaqfdVVKHmRQDQITNGMVNAISTGNWSLKRF--------KMDRqgvTQVLSRLSY---ISALGmmtriSSQFEKT 404
Cdd:CHL00207 332 NR------MTIC-DIDSLSKFNLINPKPLIALIREFfgssqlsqYMDQ---TNPLSELTHkrrISILG-----PGGLDKD 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 405 RKVSGPRSLQPSQWGMLCPSDTPEGEACGLvknlalmthittdmedgpIVKLASNLGVEDVNLLcgeELSYPNVFlvflN 484
Cdd:CHL00207 397 RISFAVRDIHPSHYGRICPIETPEGPNCGL------------------IGSLATNARINKFGFI---ETPFYKVI----N 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 485 GNILgvirdhKKLVNTfrlmrragYINEFVSISTNLTdrcvyiSSDggrlcrpyIIVKKQKpAVTNKHMEELaqgYRNfe 564
Cdd:CHL00207 452 GKVK------KFGNPI--------YLTADSEDLYRIA------PND--------INLNKNN-YFKKNIIPVR---YKQ-- 497
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 565 dflheslvEYLDVNEENDCNIAlyehtinkdtthleIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI----- 639
Cdd:CHL00207 498 --------EFKTVNPSKVDFIA--------------ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLypekp 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 640 ----GYNQRNRIDTLM------------------------------YLLAYP---------QKPMV----KTKTIEL--- 669
Cdd:CHL00207 556 ivgtGYEKQIALDSGMtiisltegivvsvsaykiiiqddnnryihyYLQKYQrsnqntcinYRPIVwvgeKINIGQIlad 635
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 670 ---IEFEKLPAGQNATVAVMSYSGYDIEDALVLNKAsldrgfgrcLVYKNAKCTLK--------RYTNQTFDKV--MGPM 736
Cdd:CHL00207 636 gsdIDNSELALGQNVLVAYMPWEGYNFEDAILINKR---------LVYEDLFTSIHiekyeielRQTKLGSEEItrNIPN 706
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 737 LDAATRKpiwrheILDADGICSPGEKVENKQVLVNKSMPTvtqiplegSNVPQQPQYK--------------DVPITYKG 802
Cdd:CHL00207 707 VSEYSLK------NLDENGIISIGSKVLAGDILVGKITPK--------GESDQLPEGKllraifgekakdvkDTSLRMPN 772
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 803 ATDSYIEKVMI----SSNAEDAFL---IKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHG 875
Cdd:CHL00207 773 GGYGRVIKVEIfsrsKGDELKFGYylkIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLG 852
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 876 FPSRMTVGKLIELLAGKAG-VLDGRFH-------YGTAFggSKV---KDVCEDLVRHGYNYL------GKDYVTSGITGE 938
Cdd:CHL00207 853 VPSRMNVGQLFECLLGLAGdNLNKRFKilpfdemYGSEY--SRIlinNKLNQASIKNNEYWLfnsyhpGKMVLRDGRTGY 930
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 939 PLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafe 1018
Cdd:CHL00207 931 KFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD--- 1007
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*...
gi 238908505 1019 vDVCGQCGLLGYsgwchYCKSSCHVSSLrIPYACKLLFQELQSMNI-IPRLKLSKYNE 1075
Cdd:CHL00207 1008 -DMQGRNETLNA-----IVKGQPIPKPG-TPESFKVLMRELQSLGLdIEAYKIENFLE 1058
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
985-1071 |
2.75e-46 |
|
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: 160.45 E-value: 2.75e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 985 GGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNI 1064
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNKCPICKGETDISPGYIPESFKLLFQELQSLGI 80
|
....*..
gi 238908505 1065 IPRLKLS 1071
Cdd:pfam04560 81 DPRLLLE 87
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
678-1015 |
2.76e-45 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 177.79 E-value: 2.76e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 678 GQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTL--KRY------TNQTFDKVMG--PMLDAAtrkpIWR 747
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLISE---------RLVYEDIYTSFhiRKYeiqthvTSQGPERITKeiPHLEAH----LLR 718
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 748 HeiLDADGICSPGEKVENKQVLVNKSMPtvtQIPLEGSNVP-----------QQPQYKD----VPITYKG-ATD-SYIEK 810
Cdd:CHL00001 719 N--LDKNGIVMLGSWVETGDILVGKLTP---QEAEESSYAPegrllraifgiQVSTSKEtclkLPIGGRGrVIDvRWIQK 793
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 811 VMISSNaeDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLA 890
Cdd:CHL00001 794 KGGSSY--NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL 871
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 891 GKAGVLDGRfHYG-TAFGGSKVKDVCEDLVRH---------GY------NYLGKDYVTSGITGEPLEAYIYFGPVYYQKL 954
Cdd:CHL00001 872 GLAGDLLNR-HYRiAPFDERYEQEASRKLVFSelyeaskqtANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKL 950
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 238908505 955 KHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSD 1015
Cdd:CHL00001 951 IHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
822-1023 |
3.11e-39 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 158.73 E-value: 3.11e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 822 LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRfH 901
Cdd:PRK00405 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGI-K 947
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 902 YGT-AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEG 980
Cdd:PRK00405 948 FATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 238908505 981 RSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCG 1023
Cdd:PRK00405 1028 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVVG 1066
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
481-542 |
2.74e-31 |
|
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: 116.70 E-value: 2.74e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 238908505 481 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 542
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
258-1062 |
1.07e-29 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 128.50 E-value: 1.07e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 258 TILTHVPVkefnfrakcIYTAVMVRRVILAQGdnKVDDRDYYGNKRLELAGQLLSllfEDLFKKFNSEMKKIADQVIPKQ 337
Cdd:PRK09603 430 TTLTHEDI---------ITTVKYLMKIKNNQG--KIDDRDHLGNRRIRAVGELLA---NELHSGLVKMQKTIKDKLTTMS 495
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 338 RAaqFDVVkhMRQDQITNGMVNA----ISTGNwSLKRFkMDRqgvTQVLSRLSY---ISALGmmtriSSQFEKTRKVSGP 410
Cdd:PRK09603 496 GA--FDSL--MPHDLVNSKMITStimeFFMGG-QLSQF-MDQ---TNPLSEVTHkrrLSALG-----EGGLVKDRVGFEA 561
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 411 RSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpivklasnlgvedvnllcgeelsypnvflvflngNILGV 490
Cdd:PRK09603 562 RDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV-----------------------------------------NDLGF 600
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 491 IR-DHKKLVNTfrlmrragyinefvsistNLTDRCVYISS---DGgrlcrpYIIVKKQKPAVTNKHMEElaqgyrnfedf 566
Cdd:PRK09603 601 IEaPYKKVVDG------------------KVVGETIYLTAiqeDS------HIIAPASTPIDEEGNILG----------- 645
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 567 lheSLVEyldvnEENDCNIALYEHTinkDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM---------- 636
Cdd:PRK09603 646 ---DLIE-----TRVEGEIVLNEKS---KVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapiv 714
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 637 -------------GTIGYNQR---NRIDTL-MYLL----------AYP--------------QKPMVKT-KTIEL----- 669
Cdd:PRK09603 715 gtgiekiiardswGAIKANRAgvvEKIDSKnIYILgegkeeayidAYSlqknlrtnqntsfnQVPIVKVgDKVEAgqiia 794
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 670 ----IEFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRK-P 744
Cdd:PRK09603 795 dgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVSE---------RITKDDIFTSTHIYEKEVDARELKHGVEEFTADiP 865
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 745 IWRHEI---LDADGICSPGEKVENKQVLVNKSMP-------------------------------------TVTQIPL-- 782
Cdd:PRK09603 866 DVKEEAlahLDESGIVKVGTYVSAGMILVGKTSPkgeikstpeerllraifgdkaghvvnkslycppslegTVIDVKVft 945
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 783 -------------------------------------------------------------EGSNVPQQ----------- 790
Cdd:PRK09603 946 kkgyekdarvlsayeeekakldmehfdrltmlnreellrvssllsqaileepfshngkdykEGDQIPKEeiasinrftla 1025
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 791 ---PQY-KDVPITYKGATDSYIE-KVMISSNAEDAF---------------LIKMLLRQTRRPEIGDKFSSRHGQKGVCG 850
Cdd:PRK09603 1026 slvKKYsKEVQNHYEITKNNFLEqKKVLGEEHEEKLsilekddilpngvikKVKLYIATKRKLKVGDKMAGRHGNKGIVS 1105
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 851 LIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIEL---LAGK----------------------------AGV---- 895
Cdd:PRK09603 1106 NIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMhlgLVGKefgkqiasmledktkdfakelrakmleiANAinek 1185
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 896 ----------LDGRFHYGTAFGGSK-VK---DVCEDLVRHGYNYL---------GKDYVTSGITGEPLEAYIYFGPVYYQ 952
Cdd:PRK09603 1186 dpltihalenCSDEELLEYAKDWSKgVKmaiPVFEGISQEKFYKLfelakiamdGKMDLYDGRTGEKMRERVNVGYMYMI 1265
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 953 KLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCGQCGllGYSG 1032
Cdd:PRK09603 1266 KLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD----DIRGREN--AYRA 1339
|
1050 1060 1070
....*....|....*....|....*....|
gi 238908505 1033 wchyCKSSCHVSSLRIPYACKLLFQELQSM 1062
Cdd:PRK09603 1340 ----IAKGEQVGESEIPETFYVLTKELQSL 1365
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
127-305 |
1.62e-26 |
|
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: 107.43 E-value: 1.62e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 127 SKNRIIVEADRKGA-VGASVTSSTHE-KKSRTNMAVKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI---GTEE 201
Cdd:pfam04561 1 RSNGIYVEKELDKNgIIATYTSSLISnRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLcydFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 202 HVMAAFgpSLEECQKAQIFTQMQALKYIGNKVRrqrmwGGGPKKTKIEEARELLAST-----ILTHVPVKE--FNFRAKC 274
Cdd:pfam04561 81 QMLELL--KPELEEAENIYTQEEALDYIGKGFA-----LRRGEEPRLQRAREILYSRdpkynLNKHLGLNEpfENERLKA 153
|
170 180 190
....*....|....*....|....*....|..
gi 238908505 275 IYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLE 305
Cdd:pfam04561 154 QDILYMIDRLLnLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
258-1015 |
3.29e-23 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 107.40 E-value: 3.29e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 258 TILTHVPVKEfnfrakciytavMVRRVILAQ-GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSEMKKIADQVIPK 336
Cdd:PRK14844 439 TVLTHEDIIE------------IVRKIVLLRdGQGSVDDIDHLGNRRVRSVGEFIE-------NQFRTGLLKLERAVVDS 499
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 337 QRAAQFDVVK---HMRQDQITNGMVNAISTGNwsLKRFkMDRQGVTQVLSRLSYISALGM--MTRISSQFEKtrkvsgpR 411
Cdd:PRK14844 500 MSTSSLDKVSpsdFINPKVLTNVLRDFFNSSQ--LSQF-MDQTNPLSEITHKRRLSALGPggLTRERAGFEV-------R 569
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 412 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITT-DMEDGPIVKLASNLGVEDVNLLCG--EELSYPNVFLVFLNGNil 488
Cdd:PRK14844 570 DVHPTHYGRICPIETPEGQNIGLINSLAIYARINKyGFIESPYRKVVNRVVTDQIEYLSAidEGLYYIADTSAKLDEN-- 647
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 489 gvirdhKKLVNTFRLMRRAGyinEFVSISTnltDRCVYISsdggrlcrpyiivkkqkpaVTNKHMEELAQgyrnfedflh 568
Cdd:PRK14844 648 ------NCFVDDMLYCRYAG---SFVMVSS---DQVSYID-------------------VSPKQVISVAA---------- 686
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 569 eSLVEYLdvnEENDCNIALYEHTINKDTTHL----------EIEPFTLLGVCA-------GLIpyphhNQSPRNTYQC-A 630
Cdd:PRK14844 687 -SLIPFL---ENDDANRALMGSNMQRQAVPLlkptaplvatGMESFVASGSGAvvlakrdGIV-----DSSDSNSIVIrA 757
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 631 MGKQAMGTIGYN-------QRNRIDTLMyllayPQKPMVKTKTI----------ELIEFEKLPAGQNATVAVMSYSGYDI 693
Cdd:PRK14844 758 FDKERVNYLDVDiyhlrkfQRSNHNTCI-----NQKPLVCVGDYvkegdviadgPAINSGELALGQNLLVAFMSWQGYNF 832
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 694 EDALVLNKASLDRGFGRCLVYKNAKCTLKrytnqtfDKVMGPmlDAATRK-PIWRHEIL---DADGICSPGEKVENKQVL 769
Cdd:PRK14844 833 EDSIIISSEVVKKDLFTSIHIEEFECVVH-------DTPLGS--EKITRAiPGVNEENLyhlDDSGIVKIGTRVGPGYIL 903
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 770 VNK-------SMPTVTQI---------------------PLEGSNVPQQ--------PQYKDVPITYKGATD-----SYI 808
Cdd:PRK14844 904 VGKvtpkpslSLPPETKLlmtifgeksfdcadsslytspDVEGTVIDVQvftrrgveENERALLIKQKEINDfekerDYI 983
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 809 ------------EKVMISSNAED--------------------------------------------------------- 819
Cdd:PRK14844 984 invtseyfydelKKLLINSGSQDrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhegydl 1063
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 820 ----AFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAG---- 891
Cdd:PRK14844 1064 pqgvSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwack 1143
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 892 -----------------------------------KAGVLDGR------------------------------------- 899
Cdd:PRK14844 1144 klgekvgnildeinkiksafckgirslnddnftkfAAAYLDNKkienidddeitasvlntpnknalndelnelvenylns 1223
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 900 ---------------FHYGT--------------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVT 932
Cdd:PRK14844 1224 cksaysnlrnflievYSCGSnvsicnnirdisdnnliefarklrdgipvaapVFEGPKDEQIAKLFELAGLDNSGQAVLY 1303
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238908505 933 SGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMI 1012
Cdd:PRK14844 1304 DGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTV 1383
|
...
gi 238908505 1013 SSD 1015
Cdd:PRK14844 1384 KSD 1386
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
380-443 |
2.75e-21 |
|
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: 88.35 E-value: 2.75e-21
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 238908505 380 QVLSRLSYISALGMMTRISS---QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 443
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSprgGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
563-603 |
5.07e-10 |
|
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: 56.01 E-value: 5.07e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 238908505 563 FEDFLHESLVEYLDVNEENDCNIALYE-----------HTINKDT-THLEIEP 603
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPedleessreerEGPYAHTyTHCEIHP 53
|
|
| |
