|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
39-997 |
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: 963.18 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 39 LVKQHIDSFNYFINVEIKKIMKANEKVTSDA-DPMWYLKYLNIYVGLPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 118 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEaDRK 196
Cdd:cd00653 80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 197 GAVGASVTSSTHEKKSRTNMAVKQGRFYLRHNTLSEDIPIviifkamgvesdqeivqmigteehvmaafgpsleecqkaq 276
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 277 iftQMQALKYIGNKVrrqrmwgggpkktkieearellastilthvpvkefnfrakcIYTAVMVRRVI-LAQGDNKVDDRD 355
Cdd:cd00653 199 ---QEEALKYIGKRF-----------------------------------------EDLIYMIRKLIlLVLGKGKLDDID 234
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 356 YYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQG 435
Cdd:cd00653 235 HLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSG 312
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 436 VTQVLSRLSYISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpivkl 514
Cdd:cd00653 313 LSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 515 asnlgvedvnllcgeelsypnvflvflngnilgvirdhkklvntfrlmrragyinefvsistnltdrcvyissdgGRLCR 594
Cdd:cd00653 382 ---------------------------------------------------------------------------GRIER 386
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 595 PYIIVKKQkpavtnkhmeelaqgyrnfedflheslveyldvneendcnialyehtinkdTTHLEIEPFTLLGVCAGLIPY 674
Cdd:cd00653 387 PYRIVEKE---------------------------------------------------VTHIEISPSQILSVAASLIPF 415
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 675 PHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDA 754
Cdd:cd00653 416 PEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDA 495
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 755 LVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPT 834
Cdd:cd00653 496 IIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDI----PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPK 571
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 835 VTQIPLEGSNVPQQpQYKDVPITYKGATDSYIEKVMISS---NAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIV 911
Cdd:cd00653 572 GETESTPIFGEKAR-DVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 912 PQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTS 991
Cdd:cd00653 651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYD 730
|
....*.
gi 1034580532 992 GITGNK 997
Cdd:cd00653 731 GRTGEP 736
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
26-997 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 868.50 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 26 KWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKAnEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLR 105
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 106 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLS 185
Cdd:PRK08565 80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 186 KNRIIVEADRKGA---VGASVTSSTHEKKSRTNMA-VKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMIGTEEHV 261
Cdd:PRK08565 160 PNRVLVDKGEAGSsitHTAKVISSRAGYRAQVTVErRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 262 MAAFGPSLEECQKAQIfTQMQALKYIGNKVRRqrmwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRR 341
Cdd:PRK08565 240 QQELLPSLEQASSIAA-TVEDALDYIGKRVAI-----GQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 342 VI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVkhMRQDQITNGMVNAIS 420
Cdd:PRK08565 314 LLeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALA 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 421 TGNWSlkrfkMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMT 500
Cdd:PRK08565 392 TGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMA 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 501 HITTDMEDGPIVKLASNLGVEDVNLLCGEElsYPNVFLVFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTD 580
Cdd:PRK08565 467 QISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETG 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 581 --RCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLE 658
Cdd:PRK08565 545 eiNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLE 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 659 IEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQN 738
Cdd:PRK08565 625 IWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQN 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 739 ATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPG 818
Cdd:PRK08565 705 AVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPE 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 819 EKVENKQVLVNK-SMPTVTQIPLEGSNVPQqpQYKDVPITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKF 897
Cdd:PRK08565 785 VEVKGGDVLIGKtSPPRFLEELEELSLGLQ--ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKF 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 898 SSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLV 977
Cdd:PRK08565 863 ASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELL 942
|
970 980
....*....|....*....|
gi 1034580532 978 RHGYNYLGKDYVTSGITGNK 997
Cdd:PRK08565 943 KLGYKPDGTEVMYDGRTGEK 962
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
539-997 |
2.87e-166 |
|
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: 501.09 E-value: 2.87e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 618
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 619 RNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 698
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 699 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 778
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 779 LKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPIT 857
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVTER--RRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 858 YKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSR 937
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 938 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGNK 997
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEK 458
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
668-997 |
5.99e-157 |
|
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: 468.16 E-value: 5.99e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 668 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYS 747
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 748 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVL 827
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 828 VNKSMPTVTQIPLEGSNVPQQPQYKDVPITYKGATDSYIEKVMI-SSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 906
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 907 CGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLVRHGYNYL 984
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330
....*....|...
gi 1034580532 985 GKDYVTSGITGNK 997
Cdd:pfam00562 315 GKEVLYDGRTGEP 327
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
31-995 |
7.21e-133 |
|
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: 426.45 E-value: 7.21e-133
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 31 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKaNEKVTSDADPMWYLKYLNIYVGLPdveesfnvtrPVSPHECRLRDMTYS 110
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFD-EISPIEDFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 111 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpaefaklnecpldpgGYFIVKGVEKVILIQEQLSKNRI 189
Cdd:COG0085 77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 190 IVEADRKGA---VGASVTSSTH-----EKKSRTNMAVKQGRfylrhntlSEDIPIVIIFKAMGVESDQEIVQMIG---TE 258
Cdd:COG0085 133 FVEEEDKSGkdlYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFGddpIQ 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 259 EHVMaafgPSLEecqKAQIFTQMQALKYIGNKVRRqrmwgGGPKKtkIEEARELLASTI-------LTHV---------- 321
Cdd:COG0085 205 EYIL----ATLE---KDNTKTQEEALLEIYRKLRP-----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklg 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 322 -PVKEFNFRAKCIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFnseMKKIADQvIPKQRAAQ 399
Cdd:COG0085 271 lDVPPEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRM---ERVVRER-MTTQDVEA 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 400 FDVVKHMRQDQITNGMVNAISTGNwsLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRISSQFEktrkVsgpRSLQPS 474
Cdd:COG0085 347 ITPQSLINIRPVVAAIKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHPS 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 475 QWGMLCPSDTPEGEACGLVKNLALMthittdmedgpivklasnlgvedvnllcgeelsypnvflvflngnilgvirdhkk 554
Cdd:COG0085 414 HYGRMCPIETPEGPNIGLIGSLALY------------------------------------------------------- 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 555 lvntfrlmrraGYINEFvsistnltdrcvyissdgGRLCRPYIIVKKQKpaVTNKhmeelaqgyrnfedflheslVEYLD 634
Cdd:COG0085 439 -----------ARVNEY------------------GFIETPYRKVENGK--VTDE--------------------IEYLT 467
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 635 VNEENDCNIALYEHTINKDT-----------------------THLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGK 691
Cdd:COG0085 468 ADEEENYYIAQANAPLDEDGnfleervlvryrgeevlvppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQR 547
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 692 QAMG-----------TIGYNQRNRIDTlmyllAYPQKPMVKT----KTIELI------EFEKLPAGQNATVAVMSYSGYD 750
Cdd:COG0085 548 QAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYN 622
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 751 IEDALVLNKASLDRGFGRCLVYKNAKCTLKRY----TNQTFDKvmgPML-DAATRKpiwrheiLDADGICSPGEKVENKQ 825
Cdd:COG0085 623 YEDAIIISERLVKDDVLTSIHIEEYEIEARDTklgpEEITRDI---PNVsEEALRN-------LDEDGIIRIGAEVKGGD 692
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 826 VLVNK-SMPTVTQIPLE-----------GSNVpqqpqyKD----VPITYKGatdsYIEKVMISSNAEDAFL-------IK 882
Cdd:COG0085 693 ILVGKvTPKGETELTPEerllraifgekAREV------RDtslrVPHGEKG----KVIDVKVFSREEGDELppgvnklVR 762
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 883 MLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGT 962
Cdd:COG0085 763 VYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATP 842
|
1050 1060 1070
....*....|....*....|....*....|...
gi 1034580532 963 AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995
Cdd:COG0085 843 VFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTG 875
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
539-600 |
3.05e-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: 3.05e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034580532 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 600
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
621-661 |
5.12e-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: 5.12e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1034580532 621 FEDFLHESLVEYLDVNEENDCNIALYE-----------HTINKDT-THLEIEP 661
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. ... |
39-997 |
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: 963.18 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 39 LVKQHIDSFNYFINVEIKKIMKANEKVTSDA-DPMWYLKYLNIYVGLPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 118 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEaDRK 196
Cdd:cd00653 80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 197 GAVGASVTSSTHEKKSRTNMAVKQGRFYLRHNTLSEDIPIviifkamgvesdqeivqmigteehvmaafgpsleecqkaq 276
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 277 iftQMQALKYIGNKVrrqrmwgggpkktkieearellastilthvpvkefnfrakcIYTAVMVRRVI-LAQGDNKVDDRD 355
Cdd:cd00653 199 ---QEEALKYIGKRF-----------------------------------------EDLIYMIRKLIlLVLGKGKLDDID 234
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 356 YYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQG 435
Cdd:cd00653 235 HLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSG 312
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 436 VTQVLSRLSYISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpivkl 514
Cdd:cd00653 313 LSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 515 asnlgvedvnllcgeelsypnvflvflngnilgvirdhkklvntfrlmrragyinefvsistnltdrcvyissdgGRLCR 594
Cdd:cd00653 382 ---------------------------------------------------------------------------GRIER 386
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 595 PYIIVKKQkpavtnkhmeelaqgyrnfedflheslveyldvneendcnialyehtinkdTTHLEIEPFTLLGVCAGLIPY 674
Cdd:cd00653 387 PYRIVEKE---------------------------------------------------VTHIEISPSQILSVAASLIPF 415
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 675 PHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDA 754
Cdd:cd00653 416 PEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDA 495
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 755 LVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPT 834
Cdd:cd00653 496 IIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDI----PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPK 571
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 835 VTQIPLEGSNVPQQpQYKDVPITYKGATDSYIEKVMISS---NAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIV 911
Cdd:cd00653 572 GETESTPIFGEKAR-DVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 912 PQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTS 991
Cdd:cd00653 651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYD 730
|
....*.
gi 1034580532 992 GITGNK 997
Cdd:cd00653 731 GRTGEP 736
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
26-997 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 868.50 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 26 KWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKAnEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLR 105
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 106 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLS 185
Cdd:PRK08565 80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 186 KNRIIVEADRKGA---VGASVTSSTHEKKSRTNMA-VKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMIGTEEHV 261
Cdd:PRK08565 160 PNRVLVDKGEAGSsitHTAKVISSRAGYRAQVTVErRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 262 MAAFGPSLEECQKAQIfTQMQALKYIGNKVRRqrmwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRR 341
Cdd:PRK08565 240 QQELLPSLEQASSIAA-TVEDALDYIGKRVAI-----GQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 342 VI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVkhMRQDQITNGMVNAIS 420
Cdd:PRK08565 314 LLeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALA 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 421 TGNWSlkrfkMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMT 500
Cdd:PRK08565 392 TGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMA 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 501 HITTDMEDGPIVKLASNLGVEDVNLLCGEElsYPNVFLVFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTD 580
Cdd:PRK08565 467 QISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETG 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 581 --RCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLE 658
Cdd:PRK08565 545 eiNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLE 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 659 IEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQN 738
Cdd:PRK08565 625 IWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQN 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 739 ATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPG 818
Cdd:PRK08565 705 AVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPE 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 819 EKVENKQVLVNK-SMPTVTQIPLEGSNVPQqpQYKDVPITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKF 897
Cdd:PRK08565 785 VEVKGGDVLIGKtSPPRFLEELEELSLGLQ--ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKF 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 898 SSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLV 977
Cdd:PRK08565 863 ASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELL 942
|
970 980
....*....|....*....|
gi 1034580532 978 RHGYNYLGKDYVTSGITGNK 997
Cdd:PRK08565 943 KLGYKPDGTEVMYDGRTGEK 962
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
539-997 |
2.87e-166 |
|
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: 501.09 E-value: 2.87e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 618
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 619 RNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 698
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 699 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 778
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 779 LKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQQpqYKDVPIT 857
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVTER--RRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 858 YKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSR 937
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 938 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGNK 997
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEK 458
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
539-997 |
2.75e-163 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 493.71 E-value: 2.75e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGY 618
Cdd:PRK07225 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 619 RNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 698
Cdd:PRK07225 87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 699 YNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 778
Cdd:PRK07225 167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 779 LKRYTNQTFDKVMGPMLD--AATRKPIWRHeiLDADGICSPGEKVENKQVLVNK-SMPTVTQIPLEGSNVPQqpQYKDVP 855
Cdd:PRK07225 247 ERRYPGGQEDRFEIPDKDvrGYRGEEAYRH--LDEDGLVNPETEVKEGDVLIGKtSPPRFLEEPDDFGISPE--KRRETS 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 856 ITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFP 935
Cdd:PRK07225 323 VTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIP 402
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034580532 936 SRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGNK 997
Cdd:PRK07225 403 SRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEK 464
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
668-997 |
5.99e-157 |
|
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: 468.16 E-value: 5.99e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 668 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYS 747
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 748 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLKRYTNQTFDKVMGPMldaaTRKPIWRHEILDADGICSPGEKVENKQVL 827
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 828 VNKSMPTVTQIPLEGSNVPQQPQYKDVPITYKGATDSYIEKVMI-SSNAEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 906
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 907 CGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLVRHGYNYL 984
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330
....*....|...
gi 1034580532 985 GKDYVTSGITGNK 997
Cdd:pfam00562 315 GKEVLYDGRTGEP 327
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
31-995 |
7.21e-133 |
|
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: 426.45 E-value: 7.21e-133
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 31 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKaNEKVTSDADPMWYLKYLNIYVGLPdveesfnvtrPVSPHECRLRDMTYS 110
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFD-EISPIEDFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 111 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpaefaklnecpldpgGYFIVKGVEKVILIQEQLSKNRI 189
Cdd:COG0085 77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 190 IVEADRKGA---VGASVTSSTH-----EKKSRTNMAVKQGRfylrhntlSEDIPIVIIFKAMGVESDQEIVQMIG---TE 258
Cdd:COG0085 133 FVEEEDKSGkdlYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFGddpIQ 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 259 EHVMaafgPSLEecqKAQIFTQMQALKYIGNKVRRqrmwgGGPKKtkIEEARELLASTI-------LTHV---------- 321
Cdd:COG0085 205 EYIL----ATLE---KDNTKTQEEALLEIYRKLRP-----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklg 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 322 -PVKEFNFRAKCIYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFnseMKKIADQvIPKQRAAQ 399
Cdd:COG0085 271 lDVPPEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRM---ERVVRER-MTTQDVEA 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 400 FDVVKHMRQDQITNGMVNAISTGNwsLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRISSQFEktrkVsgpRSLQPS 474
Cdd:COG0085 347 ITPQSLINIRPVVAAIKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHPS 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 475 QWGMLCPSDTPEGEACGLVKNLALMthittdmedgpivklasnlgvedvnllcgeelsypnvflvflngnilgvirdhkk 554
Cdd:COG0085 414 HYGRMCPIETPEGPNIGLIGSLALY------------------------------------------------------- 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 555 lvntfrlmrraGYINEFvsistnltdrcvyissdgGRLCRPYIIVKKQKpaVTNKhmeelaqgyrnfedflheslVEYLD 634
Cdd:COG0085 439 -----------ARVNEY------------------GFIETPYRKVENGK--VTDE--------------------IEYLT 467
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 635 VNEENDCNIALYEHTINKDT-----------------------THLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGK 691
Cdd:COG0085 468 ADEEENYYIAQANAPLDEDGnfleervlvryrgeevlvppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQR 547
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 692 QAMG-----------TIGYNQRNRIDTlmyllAYPQKPMVKT----KTIELI------EFEKLPAGQNATVAVMSYSGYD 750
Cdd:COG0085 548 QAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYN 622
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 751 IEDALVLNKASLDRGFGRCLVYKNAKCTLKRY----TNQTFDKvmgPML-DAATRKpiwrheiLDADGICSPGEKVENKQ 825
Cdd:COG0085 623 YEDAIIISERLVKDDVLTSIHIEEYEIEARDTklgpEEITRDI---PNVsEEALRN-------LDEDGIIRIGAEVKGGD 692
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 826 VLVNK-SMPTVTQIPLE-----------GSNVpqqpqyKD----VPITYKGatdsYIEKVMISSNAEDAFL-------IK 882
Cdd:COG0085 693 ILVGKvTPKGETELTPEerllraifgekAREV------RDtslrVPHGEKG----KVIDVKVFSREEGDELppgvnklVR 762
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 883 MLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGT 962
Cdd:COG0085 763 VYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATP 842
|
1050 1060 1070
....*....|....*....|....*....|...
gi 1034580532 963 AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995
Cdd:COG0085 843 VFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTG 875
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
24-523 |
4.39e-115 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 363.89 E-value: 4.39e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 24 EEKWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECR 103
Cdd:PRK09606 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEAR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 104 LRDMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQ 183
Cdd:PRK09606 83 LRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLED 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 184 LSKNRIIVEADRKGA---VGASVTSSTH--------EKKsrtnmavKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIV 252
Cdd:PRK09606 163 LAPNKILVEKDERYGdriEVAKVFSQRRgyralvtvERN-------RDGLLEVSFPSVPGSIPFVILMRALGLETDEEIV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 253 QMIGTEEHVMAAFGPSLEEcqkAQIFTQMQALKYIGNKVRrqrmwGGGPKKTKIEEARELLASTILTHVPVKEFNFRAKC 332
Cdd:PRK09606 236 EAVSDDPEIVKFMLENLEE---AEVDTQEEALEYIGKRVA-----PGQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKA 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 333 IYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVipKQRAAQFDVVKHMRQDQI 411
Cdd:PRK09606 308 HYLGRMAEACFeLALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERA--NMRNRELSIKTAVRSDVL 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 412 TNGMVNAISTGNWslkrfKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACG 491
Cdd:PRK09606 386 TERLEHAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCG 460
|
490 500 510
....*....|....*....|....*....|..
gi 1034580532 492 LVKNLALMTHITTDMEDGPIVKLASNLGVEDV 523
Cdd:PRK09606 461 LVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
38-413 |
2.14e-112 |
|
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: 353.22 E-value: 2.14e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 38 GLVKQHIDSFNYFINVEIKKIMKANEKVTSDADP--------MWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTY 109
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIqhpgengdKLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 110 SAPITVDIEYTR-GSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNR 188
Cdd:pfam04563 81 SAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNH 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 189 IIVEADR---KGAVGASVTSSTHE-----KKSRTNMA--VKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMIGTE 258
Cdd:pfam04563 161 PIVFKKAdpkKRGSVASVRSSAEIsvrpdSTSWVNVLeyLSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELICYD 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 259 EH---VMAAFGPSLEECQKAQIFTQMQALKYIGNKVR-RQRMwgGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIY 334
Cdd:pfam04563 241 VNdqqLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRaIFRM--GRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYF 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 335 TAVMVRRVIL-AQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAaqFDVVKHMRQDQITN 413
Cdd:pfam04563 319 IGYMIRRLLLlALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDD--LMLQLLVNAKPITS 396
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
31-997 |
4.12e-42 |
|
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: 167.53 E-value: 4.12e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 31 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKAN---EKVTSDADPM------WYLKYLNIYVGLPDVeesfnvtrpvSPHE 101
Cdd:TIGR02013 12 PEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEeglEEVFKSIFPIedytgnIELEYLSYRLGEPKY----------SVEE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 102 CRLRDMTYSAPITVDIEYT----RGSQRIIRNALPIGRMPIMlrssncvlTGKtpaefaklnecpldpgGYFIVKGVEKV 177
Cdd:TIGR02013 82 CKERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLM--------TDR----------------GTFIINGAERV 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 178 ILIQEQLSKNRIIVEADRKGAVGASVTSST----------HEKKSRTNMAVKQGRfylrhntlSEDIPIVIIFKAMGVES 247
Cdd:TIGR02013 138 VVSQLHRSPGVFFSSEKDTTKSGKVLFSARiipyrgswleFETDKKDVLYVRIDR--------KRKLPATVLLRALGYTI 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 248 DQEIVQMIGTEEHVMAAFgpsleecQKAQIFTQMQALKYIGNKVRrqrmwGGGPkkTKIEEARELLASTI-------LTH 320
Cdd:TIGR02013 210 DTLILNRLGSGEYIRNTL-------RKDPTNSEEEALVEIYRKLR-----PGEP--PTVEAARSLLENLFfdpkrydLGR 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 321 VPVKEFNFRAK-------CIYT-----AVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLsllfEDLFKKFNSEMKKIA 388
Cdd:TIGR02013 276 VGRYKLNKKLGldvpesiGVLTkediiATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELL----QNQFRVGLARMERIV 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 389 dqvipKQRAAQFDVVKHMRQDQITNGMVNAIST---GNWSLKRFkMDRqgvTQVLSRLSY---ISALGM--MTRISSQFE 460
Cdd:TIGR02013 352 -----RERMSTQDTDTLTPQDLINAKPISAAIKeffGSSQLSQF-MDQ---TNPLAELTHkrrLSALGPggLTRERAGFE 422
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 461 KtrkvsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmEDGPIvklasnlgvedvnllcgeELSYPNVflvf 540
Cdd:TIGR02013 423 V-------RDVHPTHYGRICPIETPEGPNIGLINSLSTYARVN---EYGFI------------------ETPYRKV---- 470
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 541 lngnilgviRDHKKLVntfrlmrragyinefvsistnlTDRCVYISSDGGRlcrPYIIVKKQKPAVTNKHM-EELAQG-Y 618
Cdd:TIGR02013 471 ---------KDGKVVV----------------------TDEIDYLTADEED---NYVIAQANAPLDENGRFvEDLVVArY 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 619 RNFEDFLHESLVEYLDVNeendcnialyehtinkdtthleiePFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM---- 694
Cdd:TIGR02013 517 RGEITLVSPDQVDYMDVS------------------------PKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVpllr 572
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 695 ---------------------------GTIGYNQRNRI---------DTLMYLLAYP--------------QKPMV---- 720
Cdd:TIGR02013 573 seaplvgtgmeakvardsgavivakrgGVVEYVDAKRIvirydedeeEPDGGIDIYRllkyqrsnqdtcinQRPIVsvgd 652
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 721 KTKTIELI------EFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCT--LKRYTNQTFDKVMG 792
Cdd:TIGR02013 653 RVEAGDVLadgpstDLGELALGRNVLVAFMPWNGYNYEDAILISE---------RLVKDDVFTSihIEEYEVEARDTKLG 723
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 793 P---------MLDAATRKpiwrheiLDADGICSPGEKVENKQVLVNKSMPT-VTQIPLE-----------GSNVpqqpqy 851
Cdd:TIGR02013 724 PeeitrdipnVSEEALRN-------LDENGIVRIGAEVKAGDILVGKVTPKgETELTPEekllraifgekARDV------ 790
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 852 KDVPITYKGATDSYIEKVMISSNAEDAFL-------IKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGIC 924
Cdd:TIGR02013 791 RDTSLRVPPGVEGTVIDVKVFSREQGDELppgvnklVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTP 870
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034580532 925 PDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRF--HYGTA-FGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGNK 997
Cdd:TIGR02013 871 VDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKgvPIATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQ 946
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
35-958 |
2.27e-33 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 139.46 E-value: 2.27e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 35 KVKGLVKQHIDSFNYFINVEIKKIMKANEKVTsdaDPMWYLKYLNIYvglpdveESFNVTRP-VSPHECRLRDMTYSAPI 113
Cdd:CHL00207 6 ALPDFLEIQRTSFCWFLNEGLNEELNIFSKIF---DYTGNLELLLFG-------KNYKLKYPkYNLLSAKSYDSNYSIQI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 114 TVDIEYTRGSQRIIRNA-LPIGRMPIMLRSSNCVLTGktpAEFAKLNECPLDPGGYFivkgvEKVILiqeqlSKNRIIVE 192
Cdd:CHL00207 76 YLPLKFINLKTNKIKFInYLIGNLPKMTQRGTFIING---LERVIVSQIIRSPGIYF-----KKEIK-----KNSNKIYS 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 193 ADRKGAVGASVTSSTHEKKsrtnmavkqgRFYLRHNTLSEdIPIVIIFKAMGVeSDQEIVQmigteeHVMAAFGPSLEEC 272
Cdd:CHL00207 143 ATLIPNRGSWIKFELDKNK----------EIWIRIDKNRK-KPLIIFLKALGL-TDQDIYS------RLTKSEFLKKLKP 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 273 QKAQI--FTQMQALKYIGNKVRRqrmwggGPKKTkIEEARELLASTILT----------------HVPVKEFNFRAKCIY 334
Cdd:CHL00207 205 ILLNSnsYTNEEILLEIYKNLSP------IEPAT-VNDANQNLFSRFFDpknydlgkvgrykinnKLNLNIPERVRNLTY 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 335 T---AVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSemkkiadqVIPKQraaqfdVVKHmRQDQI 411
Cdd:CHL00207 278 EdilSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLER--------ILRNR------MTIC-DIDSL 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 412 TNGMVNAISTGNWSLKRFKMDRQGV-----TQVLSRLSY---ISALGmmtriSSQFEKTRKVSGPRSLQPSQWGMLCPSD 483
Cdd:CHL00207 343 SKFNLINPKPLIALIREFFGSSQLSqymdqTNPLSELTHkrrISILG-----PGGLDKDRISFAVRDIHPSHYGRICPIE 417
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 484 TPEGEACGLvknlalmthittdmedgpIVKLASNLGVEDVNLLcgeELSYPNVFlvflNGNILgvirdhKKLVNTfrlmr 563
Cdd:CHL00207 418 TPEGPNCGL------------------IGSLATNARINKFGFI---ETPFYKVI----NGKVK------KFGNPI----- 461
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 564 ragYINEFvsistnltdrcvyiSSDGGRLCRPYIIVKKQKpAVTNKHMEELaqgYRNfedflheslvEYLDVNEENDCNI 643
Cdd:CHL00207 462 ---YLTAD--------------SEDLYRIAPNDINLNKNN-YFKKNIIPVR---YKQ----------EFKTVNPSKVDFI 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 644 AlyehtinkdtthleIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQRNRIDTLM----- 709
Cdd:CHL00207 511 A--------------ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLypekpivgtGYEKQIALDSGMtiisl 576
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 710 -------------------------YLLAYP---------QKPMV----KTKTIEL------IEFEKLPAGQNATVAVMS 745
Cdd:CHL00207 577 tegivvsvsaykiiiqddnnryihyYLQKYQrsnqntcinYRPIVwvgeKINIGQIladgsdIDNSELALGQNVLVAYMP 656
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 746 YSGYDIEDALVLNKAsldrgfgrcLVYKNAKCTLK--------RYTNQTFDKV--MGPMLDAATRKpiwrheILDADGIC 815
Cdd:CHL00207 657 WEGYNFEDAILINKR---------LVYEDLFTSIHiekyeielRQTKLGSEEItrNIPNVSEYSLK------NLDENGII 721
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 816 SPGEKVENKQVLVNKSMPTvtqiplegSNVPQQPQYK--------------DVPITYKGATDSYIEKVMI----SSNAED 877
Cdd:CHL00207 722 SIGSKVLAGDILVGKITPK--------GESDQLPEGKllraifgekakdvkDTSLRMPNGGYGRVIKVEIfsrsKGDELK 793
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 878 AFL---IKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAG-V 953
Cdd:CHL00207 794 FGYylkIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGdN 873
|
....*
gi 1034580532 954 LDGRF 958
Cdd:CHL00207 874 LNKRF 878
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
539-600 |
3.05e-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: 3.05e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034580532 539 VFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 600
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
185-363 |
2.31e-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: 107.05 E-value: 2.31e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 185 SKNRIIVEADRKGA-VGASVTSSTHE-KKSRTNMAVKQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI---GTEE 259
Cdd:pfam04561 1 RSNGIYVEKELDKNgIIATYTSSLISnRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLcydFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 260 HVMAAFgpSLEECQKAQIFTQMQALKYIGNKVRrqrmwGGGPKKTKIEEARELLAST-----ILTHVPVKE--FNFRAKC 332
Cdd:pfam04561 81 QMLELL--KPELEEAENIYTQEEALDYIGKGFA-----LRRGEEPRLQRAREILYSRdpkynLNKHLGLNEpfENERLKA 153
|
170 180 190
....*....|....*....|....*....|..
gi 1034580532 333 IYTAVMVRRVI-LAQGDNKVDDRDYYGNKRLE 363
Cdd:pfam04561 154 QDILYMIDRLLnLKLGRRKPDDIDHLGNKRVR 185
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
736-960 |
2.48e-23 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 107.30 E-value: 2.48e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 736 GQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTL--KRY------TNQTFDKVMG--PMLDAAtrkpIWR 805
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLISE---------RLVYEDIYTSFhiRKYeiqthvTSQGPERITKeiPHLEAH----LLR 718
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 806 HeiLDADGICSPGEKVENKQVLVNKSMPtvtQIPLEGSNVP-----------QQPQYKD----VPITYKG-ATD-SYIEK 868
Cdd:CHL00001 719 N--LDKNGIVMLGSWVETGDILVGKLTP---QEAEESSYAPegrllraifgiQVSTSKEtclkLPIGGRGrVIDvRWIQK 793
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 869 VMISSNaeDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLA 948
Cdd:CHL00001 794 KGGSSY--NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL 871
|
250
....*....|..
gi 1034580532 949 GKAGVLDGRfHY 960
Cdd:CHL00001 872 GLAGDLLNR-HY 882
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
438-501 |
2.62e-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: 2.62e-21
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034580532 438 QVLSRLSYISALGMMTRISS---QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 501
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSprgGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
880-997 |
6.24e-18 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 89.78 E-value: 6.24e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 880 LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRfH 959
Cdd:PRK00405 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGI-K 947
|
90 100 110
....*....|....*....|....*....|....*....
gi 1034580532 960 YGT-AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGNK 997
Cdd:PRK00405 948 FATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEP 986
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
316-952 |
5.69e-16 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 83.43 E-value: 5.69e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 316 TILTHVPVkefnfrakcIYTAVMVRRVILAQGdnKVDDRDYYGNKRLELAGQLLSllfEDLFKKFNSEMKKIADQVIPKQ 395
Cdd:PRK09603 430 TTLTHEDI---------ITTVKYLMKIKNNQG--KIDDRDHLGNRRIRAVGELLA---NELHSGLVKMQKTIKDKLTTMS 495
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 396 RAaqFDVVkhMRQDQITNGMVNA----ISTGNwSLKRFkMDRqgvTQVLSRLSY---ISALGmmtriSSQFEKTRKVSGP 468
Cdd:PRK09603 496 GA--FDSL--MPHDLVNSKMITStimeFFMGG-QLSQF-MDQ---TNPLSEVTHkrrLSALG-----EGGLVKDRVGFEA 561
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 469 RSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpivklasnlgvedvnllcgeelsypnvflvflngNILGV 548
Cdd:PRK09603 562 RDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV-----------------------------------------NDLGF 600
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 549 IR-DHKKLVNTfrlmrragyinefvsistNLTDRCVYISS---DGgrlcrpYIIVKKQKPAVTNKHMEElaqgyrnfedf 624
Cdd:PRK09603 601 IEaPYKKVVDG------------------KVVGETIYLTAiqeDS------HIIAPASTPIDEEGNILG----------- 645
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 625 lheSLVEyldvnEENDCNIALYEHTinkDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM---------- 694
Cdd:PRK09603 646 ---DLIE-----TRVEGEIVLNEKS---KVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapiv 714
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 695 -------------GTIGYNQR---NRIDTL-MYLL----------AYP--------------QKPMVKT-KTIEL----- 727
Cdd:PRK09603 715 gtgiekiiardswGAIKANRAgvvEKIDSKnIYILgegkeeayidAYSlqknlrtnqntsfnQVPIVKVgDKVEAgqiia 794
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 728 ----IEFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRK-P 802
Cdd:PRK09603 795 dgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVSE---------RITKDDIFTSTHIYEKEVDARELKHGVEEFTADiP 865
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 803 IWRHEI---LDADGICSPGEKVENKQVLVNKSMP-------------------------------------TVTQIPL-- 840
Cdd:PRK09603 866 DVKEEAlahLDESGIVKVGTYVSAGMILVGKTSPkgeikstpeerllraifgdkaghvvnkslycppslegTVIDVKVft 945
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 841 -------------------------------------------------------------EGSNVPQQ----------- 848
Cdd:PRK09603 946 kkgyekdarvlsayeeekakldmehfdrltmlnreellrvssllsqaileepfshngkdykEGDQIPKEeiasinrftla 1025
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 849 ---PQY-KDVPITYKGATDSYIE-KVMISSNAEDAF---------------LIKMLLRQTRRPEIGDKFSSRHGQKGVCG 908
Cdd:PRK09603 1026 slvKKYsKEVQNHYEITKNNFLEqKKVLGEEHEEKLsilekddilpngvikKVKLYIATKRKLKVGDKMAGRHGNKGIVS 1105
|
810 820 830 840
....*....|....*....|....*....|....*....|....
gi 1034580532 909 LIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAG 952
Cdd:PRK09603 1106 NIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVG 1149
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
316-951 |
8.53e-16 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 83.13 E-value: 8.53e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 316 TILTHVPVKEfnfrakciytavMVRRVILAQ-GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSEMKKIADQVIPK 394
Cdd:PRK14844 439 TVLTHEDIIE------------IVRKIVLLRdGQGSVDDIDHLGNRRVRSVGEFIE-------NQFRTGLLKLERAVVDS 499
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 395 QRAAQFDVVK---HMRQDQITNGMVNAISTGNwsLKRFkMDRQGVTQVLSRLSYISALGM--MTRISSQFEKtrkvsgpR 469
Cdd:PRK14844 500 MSTSSLDKVSpsdFINPKVLTNVLRDFFNSSQ--LSQF-MDQTNPLSEITHKRRLSALGPggLTRERAGFEV-------R 569
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 470 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITT-DMEDGPIVKLASNLGVEDVNLLCG--EELSYPNVFLVFLNGNil 546
Cdd:PRK14844 570 DVHPTHYGRICPIETPEGQNIGLINSLAIYARINKyGFIESPYRKVVNRVVTDQIEYLSAidEGLYYIADTSAKLDEN-- 647
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 547 gvirdhKKLVNTFRLMRRAGyinEFVSISTnltDRCVYISsdggrlcrpyiivkkqkpaVTNKHMEELAQgyrnfedflh 626
Cdd:PRK14844 648 ------NCFVDDMLYCRYAG---SFVMVSS---DQVSYID-------------------VSPKQVISVAA---------- 686
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 627 eSLVEYLdvnEENDCNIALYEHTINKDTTHL----------EIEPFTLLGVCA-------GLIpyphhNQSPRNTYQC-A 688
Cdd:PRK14844 687 -SLIPFL---ENDDANRALMGSNMQRQAVPLlkptaplvatGMESFVASGSGAvvlakrdGIV-----DSSDSNSIVIrA 757
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 689 MGKQAMGTIGYN-------QRNRIDTLMyllayPQKPMVKTKTI----------ELIEFEKLPAGQNATVAVMSYSGYDI 751
Cdd:PRK14844 758 FDKERVNYLDVDiyhlrkfQRSNHNTCI-----NQKPLVCVGDYvkegdviadgPAINSGELALGQNLLVAFMSWQGYNF 832
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 752 EDALVLNKASLDRGFGRCLVYKNAKCTLKrytnqtfDKVMGPmlDAATRK-PIWRHEIL---DADGICSPGEKVENKQVL 827
Cdd:PRK14844 833 EDSIIISSEVVKKDLFTSIHIEEFECVVH-------DTPLGS--EKITRAiPGVNEENLyhlDDSGIVKIGTRVGPGYIL 903
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 828 VNK-------SMPTVTQI---------------------PLEGSNVPQQ--------PQYKDVPITYKGATD-----SYI 866
Cdd:PRK14844 904 VGKvtpkpslSLPPETKLlmtifgeksfdcadsslytspDVEGTVIDVQvftrrgveENERALLIKQKEINDfekerDYI 983
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034580532 867 ------------EKVMISSNAED--------------------------------------------------------- 877
Cdd:PRK14844 984 invtseyfydelKKLLINSGSQDrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhegydl 1063
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034580532 878 ----AFLIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKA 951
Cdd:PRK14844 1064 pqgvSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWA 1141
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
621-661 |
5.12e-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: 5.12e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1034580532 621 FEDFLHESLVEYLDVNEENDCNIALYE-----------HTINKDT-THLEIEP 661
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPedleessreerEGPYAHTyTHCEIHP 53
|
|
| |
