|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
39-1086 |
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: 1244.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 39 LVKQHIDSFNYFINVEIKKIMKANEKVTSDA-DPMWYLKYLNIYVGLPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 118 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEaDRK 196
Cdd:cd00653 80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 197 GAVGASVTS---------STHEKKSRTNMavkqGRFYLRhntlsedIPIVIIFKALKYIGNKVrrqrmwgggpkktkiee 267
Cdd:cd00653 159 GKRIYTKTSipsyspyrgSWLEVKSDKKK----DRIYVR-------IDLKRQEEALKYIGKRF----------------- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 268 arellastilthvpvkefnfrakcIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKI 346
Cdd:cd00653 211 ------------------------EDLIYMIRKLIlLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEK 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 347 ADQVIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISS-QFEKTRKVS 425
Cdd:cd00653 267 LQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGF 344
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 426 GPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpivklasnlgvedvnllcgeelsypnvflvflngnil 505
Cdd:cd00653 345 EVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------------------------------------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 506 gvirdhkklvntfrlmrragyinefvsistnltdrcvyissdgGRLCRPYIIVKKQkpavtnkhmeelaqgyrnfedflh 585
Cdd:cd00653 382 -------------------------------------------GRIERPYRIVEKE------------------------ 394
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 586 eslveyldvneendcnvalyehtinkdTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRID 665
Cdd:cd00653 395 ---------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMD 447
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 666 TLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQT 745
Cdd:cd00653 448 TKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGP 527
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 746 FDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQpQYKDVPITYKGATDSYI 825
Cdd:cd00653 528 EEITRGDI----PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKAR-DVRDTSLKYPGGEKGIV 602
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 826 EKVMISS---NAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKL 902
Cdd:cd00653 603 DDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQL 682
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 903 IELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHAR 982
Cdd:cd00653 683 LESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHAR 762
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 983 ARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSS 1062
Cdd:cd00653 763 STGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISK 842
|
1050 1060
....*....|....*....|....
gi 1926970804 1063 LRIPYACKLLFQELQSMNIIPRLK 1086
Cdd:cd00653 843 VGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
26-1088 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1036.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 26 KWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKAnEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLR 105
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 106 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLS 185
Cdd:PRK08565 80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 186 KNRIIVEADRKGA---VGASVTSSTHEKKSRTNMA-VKQGRFYLRHNTLSEDIPIVIIFKAL------------------ 243
Cdd:PRK08565 160 PNRVLVDKGEAGSsitHTAKVISSRAGYRAQVTVErRKDGTIYVSFPAVPGKIPFVILMRALgletdrdivyavsldpei 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 244 ----------------------KYIGNKVRRqrmwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRRV 301
Cdd:PRK08565 240 qqellpsleqassiaatvedalDYIGKRVAI-----GQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 302 I-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVkhMRQDQITNGMVNAIST 380
Cdd:PRK08565 315 LeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALAT 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 381 GNWSlkrfkMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 460
Cdd:PRK08565 393 GNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 461 ITTDMEDGPIVKLASNLGVEDVNLLCGEElsYPNVFLVFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTD- 539
Cdd:PRK08565 468 ISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGe 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 540 -RCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNVALYEHTINKDTTHLEI 618
Cdd:PRK08565 546 iNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEI 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 619 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNA 698
Cdd:PRK08565 626 WPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNA 705
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 699 TVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGE 778
Cdd:PRK08565 706 VVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEV 785
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 779 KVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFS 857
Cdd:PRK08565 786 EVKGGDVLIGKtSPPRFLEELEELSLGLQE--RRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFA 863
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 858 SRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVR 937
Cdd:PRK08565 864 SRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLK 943
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 938 HGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGY 1017
Cdd:PRK08565 944 LGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGH 1023
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1926970804 1018 GASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1088
Cdd:PRK08565 1024 GAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
498-1088 |
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: 699.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 498 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 577
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 578 RNFEDFLHESLVEYLDVNEENDCNVALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 657
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 658 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 737
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 738 LKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPIT 816
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVTER--RRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 817 YKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSR 896
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 897 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 976
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 977 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1050
Cdd:TIGR03670 479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
|
570 580 590
....*....|....*....|....*....|....*...
gi 1926970804 1051 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1088
Cdd:TIGR03670 559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
627-1000 |
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: 569.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 627 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYS 706
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 707 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVL 786
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 787 VNKSMPTVTQIPLEGSNVPQQPQYKDVPITYKGATDSYIEKVMI-SSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 865
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 866 CGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLVRHGYNYL 943
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 1926970804 944 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1000
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
31-1088 |
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: 559.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 31 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKaNEKVTSDADPMWYLKYLNIYVGLPdveesfnvtrPVSPHECRLRDMTYS 110
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFD-EISPIEDFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 111 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpaefaklnecpldpgGYFIVKGVEKVILIQEQLSKNRI 189
Cdd:COG0085 77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 190 IVEADRKGA---VGASVTSSTH-----EKKSRTNMAVKQGR-------FYLR----------HNTLSEDIPIVIIFK--- 241
Cdd:COG0085 133 FVEEEDKSGkdlYSAKVIPSRGawlefETDKDGTIYVRIDRkrkipvtVLLRalgletdeeiLEAFGDDPIQEYILAtle 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 242 ---------ALKYIGNKVRRqrmwgGGPKKtkIEEARELLASTI-------LTHV-----------PVKEFNFRAKCIYT 294
Cdd:COG0085 213 kdntktqeeALLEIYRKLRP-----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVPPEDRVLTAEDI 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 295 AVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFnseMKKIADQvIPKQRAAQFDVVKHMRQDQITNG 373
Cdd:COG0085 286 VATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRM---ERVVRER-MTTQDVEAITPQSLINIRPVVAA 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 374 MVNAISTGNwsLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRISSQFEktrkVsgpRSLQPSQWGMLCPSDTPEGEA 448
Cdd:COG0085 362 IKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHPSHYGRMCPIETPEGPN 428
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 449 CGLVKNLALMthittdmedgpivklasnlgvedvnllcgeelsypnvflvflngnilgvirdhkklvntfrlmrraGYIN 528
Cdd:COG0085 429 IGLIGSLALY------------------------------------------------------------------ARVN 442
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 529 EFvsistnltdrcvyissdgGRLCRPYIIVKKQKpaVTNKhmeelaqgyrnfedflheslVEYLDVNEENDCNVALYEHT 608
Cdd:COG0085 443 EY------------------GFIETPYRKVENGK--VTDE--------------------IEYLTADEEENYYIAQANAP 482
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 609 INKDT-----------------------THLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMG----------- 654
Cdd:COG0085 483 LDEDGnfleervlvryrgeevlvppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeapllhy 562
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 655 TIGYNQRNRIDTlmyllAYPQKPMVKT----KTIELI------EFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRG 724
Cdd:COG0085 563 PLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD 637
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 725 FGRCLVYKNAKCTLKRY----TNQTFDKvmgPML-DAATRKpiwrheiLDADGICSPGEKVENKQVLVNK-SMPTVTQIP 798
Cdd:COG0085 638 VLTSIHIEEYEIEARDTklgpEEITRDI---PNVsEEALRN-------LDEDGIIRIGAEVKGGDILVGKvTPKGETELT 707
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 799 LE-----------GSNVpqqpqyKD----VPITYKGatdsYIEKVMISSNAEDAFL-------IKMLLRQTRRPEIGDKF 856
Cdd:COG0085 708 PEerllraifgekAREV------RDtslrVPHGEKG----KVIDVKVFSREEGDELppgvnklVRVYVAQKRKIEVGDKL 777
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 857 SSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLV 936
Cdd:COG0085 778 AGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLE 857
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 937 RHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIG 1016
Cdd:COG0085 858 KAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEA 937
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1926970804 1017 YGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1088
Cdd:COG0085 938 YGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
498-559 |
3.76e-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: 116.31 E-value: 3.76e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1926970804 498 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 559
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
580-620 |
1.48e-09 |
|
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: 54.47 E-value: 1.48e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1926970804 580 FEDFLHESLVEYLDVNEENDCNVALYE-----------HTINKDT-THLEIEP 620
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. ... |
39-1086 |
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: 1244.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 39 LVKQHIDSFNYFINVEIKKIMKANEKVTSDA-DPMWYLKYLNIYVGLPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 118 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEaDRK 196
Cdd:cd00653 80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 197 GAVGASVTS---------STHEKKSRTNMavkqGRFYLRhntlsedIPIVIIFKALKYIGNKVrrqrmwgggpkktkiee 267
Cdd:cd00653 159 GKRIYTKTSipsyspyrgSWLEVKSDKKK----DRIYVR-------IDLKRQEEALKYIGKRF----------------- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 268 arellastilthvpvkefnfrakcIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKI 346
Cdd:cd00653 211 ------------------------EDLIYMIRKLIlLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEK 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 347 ADQVIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISS-QFEKTRKVS 425
Cdd:cd00653 267 LQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGF 344
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 426 GPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpivklasnlgvedvnllcgeelsypnvflvflngnil 505
Cdd:cd00653 345 EVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------------------------------------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 506 gvirdhkklvntfrlmrragyinefvsistnltdrcvyissdgGRLCRPYIIVKKQkpavtnkhmeelaqgyrnfedflh 585
Cdd:cd00653 382 -------------------------------------------GRIERPYRIVEKE------------------------ 394
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 586 eslveyldvneendcnvalyehtinkdTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRID 665
Cdd:cd00653 395 ---------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMD 447
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 666 TLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQT 745
Cdd:cd00653 448 TKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGP 527
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 746 FDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQpQYKDVPITYKGATDSYI 825
Cdd:cd00653 528 EEITRGDI----PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKAR-DVRDTSLKYPGGEKGIV 602
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 826 EKVMISS---NAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKL 902
Cdd:cd00653 603 DDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQL 682
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 903 IELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHAR 982
Cdd:cd00653 683 LESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHAR 762
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 983 ARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSS 1062
Cdd:cd00653 763 STGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISK 842
|
1050 1060
....*....|....*....|....
gi 1926970804 1063 LRIPYACKLLFQELQSMNIIPRLK 1086
Cdd:cd00653 843 VGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
26-1088 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1036.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 26 KWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKAnEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLR 105
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 106 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLS 185
Cdd:PRK08565 80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 186 KNRIIVEADRKGA---VGASVTSSTHEKKSRTNMA-VKQGRFYLRHNTLSEDIPIVIIFKAL------------------ 243
Cdd:PRK08565 160 PNRVLVDKGEAGSsitHTAKVISSRAGYRAQVTVErRKDGTIYVSFPAVPGKIPFVILMRALgletdrdivyavsldpei 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 244 ----------------------KYIGNKVRRqrmwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRRV 301
Cdd:PRK08565 240 qqellpsleqassiaatvedalDYIGKRVAI-----GQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 302 I-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVkhMRQDQITNGMVNAIST 380
Cdd:PRK08565 315 LeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALAT 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 381 GNWSlkrfkMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 460
Cdd:PRK08565 393 GNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 461 ITTDMEDGPIVKLASNLGVEDVNLLCGEElsYPNVFLVFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTD- 539
Cdd:PRK08565 468 ISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGe 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 540 -RCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNVALYEHTINKDTTHLEI 618
Cdd:PRK08565 546 iNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEI 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 619 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNA 698
Cdd:PRK08565 626 WPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNA 705
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 699 TVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGE 778
Cdd:PRK08565 706 VVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEV 785
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 779 KVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFS 857
Cdd:PRK08565 786 EVKGGDVLIGKtSPPRFLEELEELSLGLQE--RRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFA 863
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 858 SRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVR 937
Cdd:PRK08565 864 SRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLK 943
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 938 HGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGY 1017
Cdd:PRK08565 944 LGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGH 1023
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1926970804 1018 GASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1088
Cdd:PRK08565 1024 GAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
498-1088 |
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: 699.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 498 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 577
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 578 RNFEDFLHESLVEYLDVNEENDCNVALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 657
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 658 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 737
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 738 LKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPIT 816
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVTER--RRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 817 YKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSR 896
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 897 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 976
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 977 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1050
Cdd:TIGR03670 479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
|
570 580 590
....*....|....*....|....*....|....*...
gi 1926970804 1051 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1088
Cdd:TIGR03670 559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
498-1087 |
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 1926970804 498 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 577
Cdd:PRK07225 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 578 RNFEDFLHESLVEYLDVNEENDCNVALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 657
Cdd:PRK07225 87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 658 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 737
Cdd:PRK07225 167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 738 LKRYTNQTFDKVMGPMLD--AATRKPIWRHeiLDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVP 814
Cdd:PRK07225 247 ERRYPGGQEDRFEIPDKDvrGYRGEEAYRH--LDEDGLVNPETEVKEGDVLIGKtSPPRFLEEPDDFGISPEK--RRETS 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 815 ITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFP 894
Cdd:PRK07225 323 VTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIP 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 895 SRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHM 974
Cdd:PRK07225 403 SRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHM 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 975 VLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------S 1048
Cdd:PRK07225 483 VANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIydkkrnR 562
|
570 580 590
....*....|....*....|....*....|....*....
gi 1926970804 1049 GWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKL 1087
Cdd:PRK07225 563 KYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
627-1000 |
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: 569.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 627 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYS 706
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 707 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVL 786
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 787 VNKSMPTVTQIPLEGSNVPQQPQYKDVPITYKGATDSYIEKVMI-SSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 865
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 866 CGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLVRHGYNYL 943
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 1926970804 944 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1000
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
31-1088 |
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: 559.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 31 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKaNEKVTSDADPMWYLKYLNIYVGLPdveesfnvtrPVSPHECRLRDMTYS 110
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFD-EISPIEDFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 111 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpaefaklnecpldpgGYFIVKGVEKVILIQEQLSKNRI 189
Cdd:COG0085 77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 190 IVEADRKGA---VGASVTSSTH-----EKKSRTNMAVKQGR-------FYLR----------HNTLSEDIPIVIIFK--- 241
Cdd:COG0085 133 FVEEEDKSGkdlYSAKVIPSRGawlefETDKDGTIYVRIDRkrkipvtVLLRalgletdeeiLEAFGDDPIQEYILAtle 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 242 ---------ALKYIGNKVRRqrmwgGGPKKtkIEEARELLASTI-------LTHV-----------PVKEFNFRAKCIYT 294
Cdd:COG0085 213 kdntktqeeALLEIYRKLRP-----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVPPEDRVLTAEDI 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 295 AVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFnseMKKIADQvIPKQRAAQFDVVKHMRQDQITNG 373
Cdd:COG0085 286 VATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRM---ERVVRER-MTTQDVEAITPQSLINIRPVVAA 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 374 MVNAISTGNwsLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRISSQFEktrkVsgpRSLQPSQWGMLCPSDTPEGEA 448
Cdd:COG0085 362 IKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHPSHYGRMCPIETPEGPN 428
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 449 CGLVKNLALMthittdmedgpivklasnlgvedvnllcgeelsypnvflvflngnilgvirdhkklvntfrlmrraGYIN 528
Cdd:COG0085 429 IGLIGSLALY------------------------------------------------------------------ARVN 442
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 529 EFvsistnltdrcvyissdgGRLCRPYIIVKKQKpaVTNKhmeelaqgyrnfedflheslVEYLDVNEENDCNVALYEHT 608
Cdd:COG0085 443 EY------------------GFIETPYRKVENGK--VTDE--------------------IEYLTADEEENYYIAQANAP 482
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 609 INKDT-----------------------THLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMG----------- 654
Cdd:COG0085 483 LDEDGnfleervlvryrgeevlvppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeapllhy 562
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 655 TIGYNQRNRIDTlmyllAYPQKPMVKT----KTIELI------EFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRG 724
Cdd:COG0085 563 PLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD 637
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 725 FGRCLVYKNAKCTLKRY----TNQTFDKvmgPML-DAATRKpiwrheiLDADGICSPGEKVENKQVLVNK-SMPTVTQIP 798
Cdd:COG0085 638 VLTSIHIEEYEIEARDTklgpEEITRDI---PNVsEEALRN-------LDEDGIIRIGAEVKGGDILVGKvTPKGETELT 707
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 799 LE-----------GSNVpqqpqyKD----VPITYKGatdsYIEKVMISSNAEDAFL-------IKMLLRQTRRPEIGDKF 856
Cdd:COG0085 708 PEerllraifgekAREV------RDtslrVPHGEKG----KVIDVKVFSREEGDELppgvnklVRVYVAQKRKIEVGDKL 777
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 857 SSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLV 936
Cdd:COG0085 778 AGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLE 857
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 937 RHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIG 1016
Cdd:COG0085 858 KAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEA 937
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1926970804 1017 YGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLS 1088
Cdd:COG0085 938 YGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
24-482 |
5.76e-96 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 314.20 E-value: 5.76e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 24 EEKWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECR 103
Cdd:PRK09606 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEAR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 104 LRDMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQ 183
Cdd:PRK09606 83 LRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLED 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 184 LSKNRIIVEADRKGA---VGASVTSSTH--------EKKsrtnmavKQGRFYLRHNTLSEDIPIVIIFKAL--------- 243
Cdd:PRK09606 163 LAPNKILVEKDERYGdriEVAKVFSQRRgyralvtvERN-------RDGLLEVSFPSVPGSIPFVILMRALgletdeeiv 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 244 -----------------------------KYIGNKVRrqrmwGGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYT 294
Cdd:PRK09606 236 eavsddpeivkfmlenleeaevdtqeealEYIGKRVA-----PGQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYL 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 295 AVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVipKQRAAQFDVVKHMRQDQITNG 373
Cdd:PRK09606 311 GRMAEACFeLALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERA--NMRNRELSIKTAVRSDVLTER 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 374 MVNAISTGNWslkrfKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVK 453
Cdd:PRK09606 389 LEHAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVK 463
|
490 500
....*....|....*....|....*....
gi 1926970804 454 NLALMTHITTDMEDGPIVKLASNLGVEDV 482
Cdd:PRK09606 464 NFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
38-372 |
4.01e-94 |
|
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: 305.84 E-value: 4.01e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 38 GLVKQHIDSFNYFINVEIKKIMKANEKVTSDADP--------MWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTY 109
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIqhpgengdKLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 110 SAPITVDIEYTR-GSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNR 188
Cdd:pfam04563 81 SAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNH 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 189 IIVEADR---KGAVGASVTSSTHE-----KKSRTNMA--VKQGRFYLRHNTLSEDIPIVIIFKAL--------------- 243
Cdd:pfam04563 161 PIVFKKAdpkKRGSVASVRSSAEIsvrpdSTSWVNVLeyLSNGTIYFKFPYIKKEIPIVIILRALgftsdreifelicyd 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 244 -----------------------------KYIGNKVR-RQRMwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIY 293
Cdd:pfam04563 241 vndqqlqeellpsleegfkiriqtqeqalDYIGGRGRaIFRM--GRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYF 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 294 TAVMVRRVIL-AQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAaqFDVVKHMRQDQITN 372
Cdd:pfam04563 319 IGYMIRRLLLlALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDD--LMLQLLVNAKPITS 396
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
31-1079 |
2.33e-63 |
|
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: 234.56 E-value: 2.33e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 31 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKAN---EKVTSDADPM------WYLKYLNIYVGLPDVeesfnvtrpvSPHE 101
Cdd:TIGR02013 12 PEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEeglEEVFKSIFPIedytgnIELEYLSYRLGEPKY----------SVEE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 102 CRLRDMTYSAPITVDIEYT----RGSQRIIRNALPIGRMPIMLRSSNCVLTGktpAEFAKLNECPLDPGGYF------IV 171
Cdd:TIGR02013 82 CKERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLMTDRGTFIING---AERVVVSQLHRSPGVFFssekdtTK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 172 KGVE----KVI------LIQEQLSKNRIIVEADRKGAVGASV-------------TSSTHEKKSRTNMAVKQgrfylrhN 228
Cdd:TIGR02013 159 SGKVlfsaRIIpyrgswLEFETDKKDVLYVRIDRKRKLPATVllralgytidtliLNRLGSGEYIRNTLRKD-------P 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 229 TLSEDIPIVIIFKALK-----------------------YIGNKVRRQRMwgggPKKTKIEEArelLASTILTHVPVkef 285
Cdd:TIGR02013 232 TNSEEEALVEIYRKLRpgepptveaarsllenlffdpkrYDLGRVGRYKL----NKKLGLDVP---ESIGVLTKEDI--- 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 286 nfrakciyTAVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLsllfEDLFKKFNSEMKKIAdqvipKQRAAQFDVVKHM 365
Cdd:TIGR02013 302 --------IATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELL----QNQFRVGLARMERIV-----RERMSTQDTDTLT 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 366 RQDQITNGMVNAIST---GNWSLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRISSQFEKtrkvsgpRSLQPSQWGM 437
Cdd:TIGR02013 365 PQDLINAKPISAAIKeffGSSQLSQF-MDQ---TNPLAELTHkrrLSALGPggLTRERAGFEV-------RDVHPTHYGR 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 438 LCPSDTPEGEACGLVKNLALMTHITtdmEDGPIvklasnlgvedvnllcgeELSYPNVflvflngnilgviRDHKKLVnt 517
Cdd:TIGR02013 434 ICPIETPEGPNIGLINSLSTYARVN---EYGFI------------------ETPYRKV-------------KDGKVVV-- 477
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 518 frlmrragyinefvsistnlTDRCVYISSDGGRlcrPYIIVKKQKPAVTNKHM-EELAQG-YRNFEDFLHESLVEYLDVN 595
Cdd:TIGR02013 478 --------------------TDEIDYLTADEED---NYVIAQANAPLDENGRFvEDLVVArYRGEITLVSPDQVDYMDVS 534
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 596 eendcnvalyehtinkdtthleiePFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM---------------------- 653
Cdd:TIGR02013 535 ------------------------PKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvards 590
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 654 ---------GTIGYNQRNRI---------DTLMYLLAYP--------------QKPMV----KTKTIELI------EFEK 691
Cdd:TIGR02013 591 gavivakrgGVVEYVDAKRIvirydedeeEPDGGIDIYRllkyqrsnqdtcinQRPIVsvgdRVEAGDVLadgpstDLGE 670
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 692 LPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCT--LKRYTNQTFDKVMGP---------MLDAATRK 760
Cdd:TIGR02013 671 LALGRNVLVAFMPWNGYNYEDAILISE---------RLVKDDVFTSihIEEYEVEARDTKLGPeeitrdipnVSEEALRN 741
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 761 piwrheiLDADGICSPGEKVENKQVLVNKSMPT-VTQIPLE-----------GSNVpqqpqyKDVPITYKGATDSYIEKV 828
Cdd:TIGR02013 742 -------LDENGIVRIGAEVKAGDILVGKVTPKgETELTPEekllraifgekARDV------RDTSLRVPPGVEGTVIDV 808
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 829 MISSNAEDAFL-------IKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGK 901
Cdd:TIGR02013 809 KVFSREQGDELppgvnklVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQ 888
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 902 LIELLAGKAGVLDGRF--HYGTA-FGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDK 978
Cdd:TIGR02013 889 ILETHLGWAGKRLGRKgvPIATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDK 968
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 979 MHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSD-------AFEVDVCGQcgllgysgwc 1051
Cdd:TIGR02013 969 MHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvvgrtkAYEAIVKGE---------- 1038
|
1210 1220
....*....|....*....|....*...
gi 1926970804 1052 hycksscHVSSLRIPYACKLLFQELQSM 1079
Cdd:TIGR02013 1039 -------NVPEPGIPESFNVLIKELQSL 1059
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
35-1092 |
3.36e-55 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 209.18 E-value: 3.36e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 35 KVKGLVKQHIDSFNYFINVEIKKIMKANEKVTsdaDPMWYLKYLNIYvglpdveESFNVTRP-VSPHECRLRDMTYSAPI 113
Cdd:CHL00207 6 ALPDFLEIQRTSFCWFLNEGLNEELNIFSKIF---DYTGNLELLLFG-------KNYKLKYPkYNLLSAKSYDSNYSIQI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 114 TVDIEYTRGSQRIIRNA-LPIGRMPIMLRSSNCVLTGktpAEFAKLNECPLDPGGYF--IVKGVEKVIL----------- 179
Cdd:CHL00207 76 YLPLKFINLKTNKIKFInYLIGNLPKMTQRGTFIING---LERVIVSQIIRSPGIYFkkEIKKNSNKIYsatlipnrgsw 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 180 IQEQLSKNR-IIVEADRKGAVGASV-------TSSTHEKKSRTNMAVKQGRFYLR-HNTLSEDIPIVIIFKALKYIGNK- 249
Cdd:CHL00207 153 IKFELDKNKeIWIRIDKNRKKPLIIflkalglTDQDIYSRLTKSEFLKKLKPILLnSNSYTNEEILLEIYKNLSPIEPAt 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 250 --VRRQRMWGGGPKKTKIEEAReLLASTILTHVPVKEFNFRAKCIYT---AVMVRRVILAQGDNKVDDRDYYGNKRLELA 324
Cdd:CHL00207 233 vnDANQNLFSRFFDPKNYDLGK-VGRYKINNKLNLNIPERVRNLTYEdilSIIDKLINLKINKGNFDDIDHLKNRRVRSV 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 325 GQLLSLLFEDLFKKFNSemkkiadqVIPKQraaqfdVVKHmRQDQITNGMVNAISTGNWSLKRFKMDRQGV-----TQVL 399
Cdd:CHL00207 312 GELLQNQFRIGLKRLER--------ILRNR------MTIC-DIDSLSKFNLINPKPLIALIREFFGSSQLSqymdqTNPL 376
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 400 SRLSY---ISALGmmtriSSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLvknlalmthittdmedgpIVKLASN 476
Cdd:CHL00207 377 SELTHkrrISILG-----PGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGL------------------IGSLATN 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 477 LGVEDVNLLcgeELSYPNVFlvflNGNILgvirdhKKLVNTfrlmrragYINEFVSISTNLTdrcvyiSSDggrlcrpyI 556
Cdd:CHL00207 434 ARINKFGFI---ETPFYKVI----NGKVK------KFGNPI--------YLTADSEDLYRIA------PND--------I 478
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 557 IVKKQKpAVTNKHMEELaqgYRNfedflheslvEYLDVN-EENDcnvalyehTINkdtthleIEPFTLLGVCAGLIPYPH 635
Cdd:CHL00207 479 NLNKNN-YFKKNIIPVR---YKQ----------EFKTVNpSKVD--------FIA-------ISPIQVFSIAESLIPFLE 529
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 636 HNQSPRNTYQCAMGKQAMGTI---------GYNQRNRIDTLM------------------------------YLLAYP-- 674
Cdd:CHL00207 530 HNDANRALMGSNMQRQAVPLLypekpivgtGYEKQIALDSGMtiisltegivvsvsaykiiiqddnnryihyYLQKYQrs 609
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 675 -------QKPMV----KTKTIEL------IEFEKLPAGQNATVAVMSYSGYDIEDALVLNKAsldrgfgrcLVYKNAKCT 737
Cdd:CHL00207 610 nqntcinYRPIVwvgeKINIGQIladgsdIDNSELALGQNVLVAYMPWEGYNFEDAILINKR---------LVYEDLFTS 680
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 738 LK--------RYTNQTFDKV--MGPMLDAATRKpiwrheILDADGICSPGEKVENKQVLVNKSMPTvtqiplegSNVPQQ 807
Cdd:CHL00207 681 IHiekyeielRQTKLGSEEItrNIPNVSEYSLK------NLDENGIISIGSKVLAGDILVGKITPK--------GESDQL 746
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 808 PQYK--------------DVPITYKGATDSYIEKVMI----SSNAEDAFL---IKMLLRQTRRPEIGDKFSSRHGQKGVC 866
Cdd:CHL00207 747 PEGKllraifgekakdvkDTSLRMPNGGYGRVIKVEIfsrsKGDELKFGYylkIRVFIAQIRKIQVGDKLAGRHGNKGII 826
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 867 GLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAG-VLDGRFH-------YGTAFggSKV---KDVCEDL 935
Cdd:CHL00207 827 SRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGdNLNKRFKilpfdemYGSEY--SRIlinNKLNQAS 904
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 936 VRHGYNYL------GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEM 1009
Cdd:CHL00207 905 IKNNEYWLfnsyhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEM 984
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 1010 ERDCLIGYGASMLLLERLMISSDafevDVCGQCGLLGYsgwchYCKSSCHVSSLrIPYACKLLFQELQSMNI-IPRLKLS 1088
Cdd:CHL00207 985 EVWALEAFGAAYTLKELLTIKSD----DMQGRNETLNA-----IVKGQPIPKPG-TPESFKVLMRELQSLGLdIEAYKIE 1054
|
....
gi 1926970804 1089 KYNE 1092
Cdd:CHL00207 1055 NFLE 1058
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1002-1088 |
1.69e-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: 161.22 E-value: 1.69e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 1002 GGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNI 1081
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNKCPICKGETDISPGYIPESFKLLFQELQSLGI 80
|
....*..
gi 1926970804 1082 IPRLKLS 1088
Cdd:pfam04560 81 DPRLLLE 87
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
695-1032 |
3.01e-45 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 177.79 E-value: 3.01e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 695 GQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTL--KRY------TNQTFDKVMG--PMLDAAtrkpIWR 764
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLISE---------RLVYEDIYTSFhiRKYeiqthvTSQGPERITKeiPHLEAH----LLR 718
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 765 HeiLDADGICSPGEKVENKQVLVNKSMPtvtQIPLEGSNVP-----------QQPQYKD----VPITYKG-ATD-SYIEK 827
Cdd:CHL00001 719 N--LDKNGIVMLGSWVETGDILVGKLTP---QEAEESSYAPegrllraifgiQVSTSKEtclkLPIGGRGrVIDvRWIQK 793
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 828 VMISSNaeDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLA 907
Cdd:CHL00001 794 KGGSSY--NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL 871
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 908 GKAGVLDGRfHYG-TAFGGSKVKDVCEDLVRH---------GY------NYLGKDYVTSGITGEPLEAYIYFGPVYYQKL 971
Cdd:CHL00001 872 GLAGDLLNR-HYRiAPFDERYEQEASRKLVFSelyeaskqtANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKL 950
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1926970804 972 KHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSD 1032
Cdd:CHL00001 951 IHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
839-1040 |
3.60e-39 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 158.34 E-value: 3.60e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 839 LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRfH 918
Cdd:PRK00405 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGI-K 947
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 919 YGT-AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEG 997
Cdd:PRK00405 948 FATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1926970804 998 RSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCG 1040
Cdd:PRK00405 1028 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVVG 1066
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
498-559 |
3.76e-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: 116.31 E-value: 3.76e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1926970804 498 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 559
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
275-1079 |
1.56e-29 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 128.12 E-value: 1.56e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 275 TILTHVPVkefnfrakcIYTAVMVRRVILAQGdnKVDDRDYYGNKRLELAGQLLSllfEDLFKKFNSEMKKIADQVIPKQ 354
Cdd:PRK09603 430 TTLTHEDI---------ITTVKYLMKIKNNQG--KIDDRDHLGNRRIRAVGELLA---NELHSGLVKMQKTIKDKLTTMS 495
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 355 RAaqFDVVkhMRQDQITNGMVNA----ISTGNwSLKRFkMDRqgvTQVLSRLSY---ISALGmmtriSSQFEKTRKVSGP 427
Cdd:PRK09603 496 GA--FDSL--MPHDLVNSKMITStimeFFMGG-QLSQF-MDQ---TNPLSEVTHkrrLSALG-----EGGLVKDRVGFEA 561
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 428 RSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpivklasnlgvedvnllcgeelsypnvflvflngNILGV 507
Cdd:PRK09603 562 RDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV-----------------------------------------NDLGF 600
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 508 IR-DHKKLVNTfrlmrragyinefvsistNLTDRCVYISS---DGgrlcrpYIIVKKQKPAVTNKHMeelaqgyrnFEDF 583
Cdd:PRK09603 601 IEaPYKKVVDG------------------KVVGETIYLTAiqeDS------HIIAPASTPIDEEGNI---------LGDL 647
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 584 LHESLVEYLDVNEENDcnvalyehtinkdTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM---------- 653
Cdd:PRK09603 648 IETRVEGEIVLNEKSK-------------VTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapiv 714
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 654 -------------GTIGYNQR---NRIDTL-MYLL----------AYP--------------QKPMVKT-KTIEL----- 686
Cdd:PRK09603 715 gtgiekiiardswGAIKANRAgvvEKIDSKnIYILgegkeeayidAYSlqknlrtnqntsfnQVPIVKVgDKVEAgqiia 794
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 687 ----IEFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRK-P 761
Cdd:PRK09603 795 dgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVSE---------RITKDDIFTSTHIYEKEVDARELKHGVEEFTADiP 865
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 762 IWRHEI---LDADGICSPGEKVENKQVLVNKSMP-------------------------------------TVTQIPL-- 799
Cdd:PRK09603 866 DVKEEAlahLDESGIVKVGTYVSAGMILVGKTSPkgeikstpeerllraifgdkaghvvnkslycppslegTVIDVKVft 945
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 800 -------------------------------------------------------------EGSNVPQQ----------- 807
Cdd:PRK09603 946 kkgyekdarvlsayeeekakldmehfdrltmlnreellrvssllsqaileepfshngkdykEGDQIPKEeiasinrftla 1025
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 808 ---PQY-KDVPITYKGATDSYIE-KVMISSNAEDAF---------------LIKMLLRQTRRPEIGDKFSSRHGQKGVCG 867
Cdd:PRK09603 1026 slvKKYsKEVQNHYEITKNNFLEqKKVLGEEHEEKLsilekddilpngvikKVKLYIATKRKLKVGDKMAGRHGNKGIVS 1105
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 868 LIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIEL---LAGK----------------------------AGV---- 912
Cdd:PRK09603 1106 NIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMhlgLVGKefgkqiasmledktkdfakelrakmleiANAinek 1185
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 913 ----------LDGRFHYGTAFGGSK-VK---DVCEDLVRHGYNYL---------GKDYVTSGITGEPLEAYIYFGPVYYQ 969
Cdd:PRK09603 1186 dpltihalenCSDEELLEYAKDWSKgVKmaiPVFEGISQEKFYKLfelakiamdGKMDLYDGRTGEKMRERVNVGYMYMI 1265
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 970 KLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCGQCGllGYSG 1049
Cdd:PRK09603 1266 KLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD----DIRGREN--AYRA 1339
|
1050 1060 1070
....*....|....*....|....*....|
gi 1926970804 1050 wchyCKSSCHVSSLRIPYACKLLFQELQSM 1079
Cdd:PRK09603 1340 ----IAKGEQVGESEIPETFYVLTKELQSL 1365
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
275-1032 |
2.93e-23 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 107.79 E-value: 2.93e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 275 TILTHVPVKEfnfrakciytavMVRRVILAQ-GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSEMKKIADQVIPK 353
Cdd:PRK14844 439 TVLTHEDIIE------------IVRKIVLLRdGQGSVDDIDHLGNRRVRSVGEFIE-------NQFRTGLLKLERAVVDS 499
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 354 QRAAQFDVVK---HMRQDQITNGMVNAISTGNwsLKRFkMDRQGVTQVLSRLSYISALGM--MTRISSQFEKtrkvsgpR 428
Cdd:PRK14844 500 MSTSSLDKVSpsdFINPKVLTNVLRDFFNSSQ--LSQF-MDQTNPLSEITHKRRLSALGPggLTRERAGFEV-------R 569
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 429 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITT-DMEDGPIVKLASNLGVEDVNLLCG--EELSYPNVFLVFLNGNil 505
Cdd:PRK14844 570 DVHPTHYGRICPIETPEGQNIGLINSLAIYARINKyGFIESPYRKVVNRVVTDQIEYLSAidEGLYYIADTSAKLDEN-- 647
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 506 gvirdhKKLVNTFRLMRRAGyinEFVSISTnltDRCVYISsdggrlcrpyiivkkqkpaVTNKHMEELAQgyrnfedflh 585
Cdd:PRK14844 648 ------NCFVDDMLYCRYAG---SFVMVSS---DQVSYID-------------------VSPKQVISVAA---------- 686
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 586 eSLVEYLdvnEENDCNVALYEHTINKDTTHL----------EIEPFTLLGVCA-------GLIpyphhNQSPRNTYQC-A 647
Cdd:PRK14844 687 -SLIPFL---ENDDANRALMGSNMQRQAVPLlkptaplvatGMESFVASGSGAvvlakrdGIV-----DSSDSNSIVIrA 757
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 648 MGKQAMGTIGYN-------QRNRIDTLMyllayPQKPMVKTKTI----------ELIEFEKLPAGQNATVAVMSYSGYDI 710
Cdd:PRK14844 758 FDKERVNYLDVDiyhlrkfQRSNHNTCI-----NQKPLVCVGDYvkegdviadgPAINSGELALGQNLLVAFMSWQGYNF 832
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 711 EDALVLNKASLDRGFGRCLVYKNAKCTLKrytnqtfDKVMGPmlDAATRK-PIWRHEIL---DADGICSPGEKVENKQVL 786
Cdd:PRK14844 833 EDSIIISSEVVKKDLFTSIHIEEFECVVH-------DTPLGS--EKITRAiPGVNEENLyhlDDSGIVKIGTRVGPGYIL 903
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 787 VNK-------SMPTVTQI---------------------PLEGSNVPQQ--------PQYKDVPITYKGATD-----SYI 825
Cdd:PRK14844 904 VGKvtpkpslSLPPETKLlmtifgeksfdcadsslytspDVEGTVIDVQvftrrgveENERALLIKQKEINDfekerDYI 983
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 826 ------------EKVMISSNAED--------------------------------------------------------- 836
Cdd:PRK14844 984 invtseyfydelKKLLINSGSQDrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhegydl 1063
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 837 ----AFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAG---- 908
Cdd:PRK14844 1064 pqgvSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwack 1143
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 909 -----------------------------------KAGVLDGR------------------------------------- 916
Cdd:PRK14844 1144 klgekvgnildeinkiksafckgirslnddnftkfAAAYLDNKkienidddeitasvlntpnknalndelnelvenylns 1223
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 917 ---------------FHYGT--------------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVT 949
Cdd:PRK14844 1224 cksaysnlrnflievYSCGSnvsicnnirdisdnnliefarklrdgipvaapVFEGPKDEQIAKLFELAGLDNSGQAVLY 1303
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 950 SGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMI 1029
Cdd:PRK14844 1304 DGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTV 1383
|
...
gi 1926970804 1030 SSD 1032
Cdd:PRK14844 1384 KSD 1386
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
397-460 |
2.80e-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: 2.80e-21
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1926970804 397 QVLSRLSYISALGMMTRISS---QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 460
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSprgGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
185-322 |
5.85e-13 |
|
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: 68.53 E-value: 5.85e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 185 SKNRIIVEADRKGA-VGASVTSSTHE-KKSRTNMAVKQGRFYLRHNTLSEDIPIVIIFKAL------------------- 243
Cdd:pfam04561 1 RSNGIYVEKELDKNgIIATYTSSLISnRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALglvsdreildrlcydfndp 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1926970804 244 -----------------------KYIGNKVRrqrmwGGGPKKTKIEEARELLAST-----ILTHVPVKE--FNFRAKCIY 293
Cdd:pfam04561 81 qmlellkpeleeaeniytqeealDYIGKGFA-----LRRGEEPRLQRAREILYSRdpkynLNKHLGLNEpfENERLKAQD 155
|
170 180 190
....*....|....*....|....*....|
gi 1926970804 294 TAVMVRRVI-LAQGDNKVDDRDYYGNKRLE 322
Cdd:pfam04561 156 ILYMIDRLLnLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
580-620 |
1.48e-09 |
|
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: 54.47 E-value: 1.48e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1926970804 580 FEDFLHESLVEYLDVNEENDCNVALYE-----------HTINKDT-THLEIEP 620
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPedleessreerEGPYAHTyTHCEIHP 53
|
|
| |
